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+                <td>2544</td>
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-		<source>/home/user/actions-runner/_work/biobb_analysis/biobb_analysis</source>
+		<source>/home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis</source>
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index d4a473d..2ecc5a2 100644
--- a/coverage/function_index.html
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@@ -1747,10 +1747,10 @@ <h2>
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                 <td>0</td>
-                <td class="right" data-ratio="11 16">69%</td>
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             <tr class="region">
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-                <td>2545</td>
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-                <td class="right" data-ratio="2007 2545">79%</td>
+                <td class="right" data-ratio="2006 2544">79%</td>
             </tr>
         </tfoot>
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     </div>
     <aside class="hidden">
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index d8e8fba..70424f4 100644
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         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
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             <tr class="region">
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             <a id="nextFileLink" class="nav" href="z_018feecd41fcf543_test_gmx_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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 </footer>
diff --git a/coverage/z_018feecd41fcf543_test_gmx_image_py.html b/coverage/z_018feecd41fcf543_test_gmx_image_py.html
index 7d1e377..40ac8f6 100644
--- a/coverage/z_018feecd41fcf543_test_gmx_image_py.html
+++ b/coverage/z_018feecd41fcf543_test_gmx_image_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_018feecd41fcf543_test_gmx_rgyr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -110,7 +110,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_rgyr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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 </footer>
diff --git a/coverage/z_018feecd41fcf543_test_gmx_rgyr_py.html b/coverage/z_018feecd41fcf543_test_gmx_rgyr_py.html
index 6faa2f8..55b50f6 100644
--- a/coverage/z_018feecd41fcf543_test_gmx_rgyr_py.html
+++ b/coverage/z_018feecd41fcf543_test_gmx_rgyr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_018feecd41fcf543_test_gmx_rms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_rms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_018feecd41fcf543_test_gmx_rms_py.html b/coverage/z_018feecd41fcf543_test_gmx_rms_py.html
index 5bb8ea4..0067602 100644
--- a/coverage/z_018feecd41fcf543_test_gmx_rms_py.html
+++ b/coverage/z_018feecd41fcf543_test_gmx_rms_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_018feecd41fcf543_test_gmx_trjconv_str_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_trjconv_str_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_ens_py.html b/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_ens_py.html
index f03c82b..939a65d 100644
--- a/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_ens_py.html
+++ b/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_ens_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_018feecd41fcf543_test_gmx_trjconv_trj_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_trjconv_trj_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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 </footer>
diff --git a/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_py.html b/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_py.html
index 5c9bb84..f71522d 100644
--- a/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_py.html
+++ b/coverage/z_018feecd41fcf543_test_gmx_trjconv_str_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_018feecd41fcf543_test_gmx_trjconv_str_ens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_trjconv_str_ens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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     </div>
 </footer>
diff --git a/coverage/z_018feecd41fcf543_test_gmx_trjconv_trj_py.html b/coverage/z_018feecd41fcf543_test_gmx_trjconv_trj_py.html
index b5fe879..26ced73 100644
--- a/coverage/z_018feecd41fcf543_test_gmx_trjconv_trj_py.html
+++ b/coverage/z_018feecd41fcf543_test_gmx_trjconv_trj_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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     </div>
 </footer>
diff --git a/coverage/z_153b2b1bc44effd1___init___py.html b/coverage/z_153b2b1bc44effd1___init___py.html
index 1482f5a..ff3af97 100644
--- a/coverage/z_153b2b1bc44effd1___init___py.html
+++ b/coverage/z_153b2b1bc44effd1___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -104,7 +104,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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     </div>
 </footer>
diff --git a/coverage/z_153b2b1bc44effd1_common_py.html b/coverage/z_153b2b1bc44effd1_common_py.html
index b6fd18b..b98e539 100644
--- a/coverage/z_153b2b1bc44effd1_common_py.html
+++ b/coverage/z_153b2b1bc44effd1_common_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_cpptraj_average_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -499,17 +499,17 @@ <h2>
     <p class="pln"><span class="n"><a id="t417" href="#t417">417</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t418" href="#t418">418</a></span><span class="t">    <span class="key">if</span> <span class="nam">ref</span> <span class="op">==</span> <span class="str">'first'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t419" href="#t419">419</a></span><span class="t">        <span class="key">if</span> <span class="nam">output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t420" href="#t420">420</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t420" href="#t420">420</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t421" href="#t421">421</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t422" href="#t422">422</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first'</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t422" href="#t422">422</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first'</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t423" href="#t423">423</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t424" href="#t424">424</a></span><span class="t">    <span class="key">if</span> <span class="nam">ref</span> <span class="op">==</span> <span class="str">'average'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t425" href="#t425">425</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'average crdset '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t426" href="#t426">426</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'run'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t427" href="#t427">427</a></span><span class="t">        <span class="key">if</span> <span class="nam">output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t428" href="#t428">428</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t428" href="#t428">428</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t429" href="#t429">429</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t430" href="#t430">430</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t430" href="#t430">430</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t431" href="#t431">431</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t432" href="#t432">432</a></span><span class="t">    <span class="key">if</span> <span class="nam">ref</span> <span class="op">==</span> <span class="str">'experimental'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t433" href="#t433">433</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">input_exp_path</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -520,9 +520,9 @@ <h2>
     <p class="run"><span class="n"><a id="t438" href="#t438">438</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'reference '</span> <span class="op">+</span> <span class="nam">input_exp_path</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">solute</span> <span class="op">+</span> <span class="str">' parm [exp]'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t439" href="#t439">439</a></span><span class="t">        <span class="nam">backbone</span><span class="op">,</span> <span class="nam">msg</span> <span class="op">=</span> <span class="nam">get_mask_atoms</span><span class="op">(</span><span class="str">'backbone'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t440" href="#t440">440</a></span><span class="t">        <span class="key">if</span> <span class="nam">output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t441" href="#t441">441</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t441" href="#t441">441</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t442" href="#t442">442</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t443" href="#t443">443</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t443" href="#t443">443</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t444" href="#t444">444</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t445" href="#t445">445</a></span><span class="t">    <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t446" href="#t446">446</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -565,7 +565,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_average_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_average_py.html
index c2149f3..8a54f19 100644
--- a/coverage/z_153b2b1bc44effd1_cpptraj_average_py.html
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@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -303,7 +303,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_cpptraj_bfactor_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_bfactor_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_bfactor_py.html
index 345aa61..3a399a6 100644
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+++ b/coverage/z_153b2b1bc44effd1_cpptraj_bfactor_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_cpptraj_convert_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -313,7 +313,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_cpptraj_convert_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_convert_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_convert_py.html
index c23e09c..a579eb0 100644
--- a/coverage/z_153b2b1bc44effd1_cpptraj_convert_py.html
+++ b/coverage/z_153b2b1bc44effd1_cpptraj_convert_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_cpptraj_dry_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -300,7 +300,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_dry_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_dry_py.html
index 1f3255e..90bd534 100644
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@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -306,7 +306,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_cpptraj_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_image_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_image_py.html
index 86d5cbf..59dbc79 100644
--- a/coverage/z_153b2b1bc44effd1_cpptraj_image_py.html
+++ b/coverage/z_153b2b1bc44effd1_cpptraj_image_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_cpptraj_input_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -306,7 +306,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_cpptraj_input_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_input_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_input_py.html
index a584175..d3a94e9 100644
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@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_cpptraj_mask_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -220,7 +220,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_cpptraj_mask_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_mask_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_mask_py.html
index 9fcde55..7b30a1f 100644
--- a/coverage/z_153b2b1bc44effd1_cpptraj_mask_py.html
+++ b/coverage/z_153b2b1bc44effd1_cpptraj_mask_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_153b2b1bc44effd1_cpptraj_rgyr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -305,7 +305,7 @@ <h2>
             <a class="nav" href="z_153b2b1bc44effd1_cpptraj_rgyr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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     </div>
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_rgyr_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_rgyr_py.html
index 08abb3f..84b6aea 100644
--- a/coverage/z_153b2b1bc44effd1_cpptraj_rgyr_py.html
+++ b/coverage/z_153b2b1bc44effd1_cpptraj_rgyr_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -298,7 +298,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_153b2b1bc44effd1_cpptraj_rms_py.html b/coverage/z_153b2b1bc44effd1_cpptraj_rms_py.html
index 21f84db..790bbb8 100644
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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+            created at 2025-01-08 09:46 +0000
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+            created at 2025-01-08 09:46 +0000
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index d8644ac..d69dcb8 100644
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             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -134,7 +134,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_convert_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_convert_py.html
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@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_dry_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_dry_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_dry_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_dry_py.html
index 0267d12..a15bcab 100644
--- a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_dry_py.html
+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_dry_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_image_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_image_py.html
index 51cd18a..e9e7f6d 100644
--- a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_image_py.html
+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_image_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_input_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_input_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_input_py.html
index 386e5d3..615ae8a 100644
--- a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_input_py.html
+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_input_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_mask_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_mask_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_mask_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_mask_py.html
index 0b14236..ba039f6 100644
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rgyr_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rgyr_py.html
index 579102b..0a7aaff 100644
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@@ -65,7 +65,7 @@ <h2>
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
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+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rms_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rms_py.html
index 3d88c9d..6b24dfa 100644
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+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rms_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_rmsf_py.html">&#xbb; next</a>
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -140,7 +140,7 @@ <h2>
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+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rmsf_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rmsf_py.html
index 0d7ca56..94211ae 100644
--- a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_rmsf_py.html
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@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -134,7 +134,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_slice_py.html">&#xbb; next</a>
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+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_slice_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_slice_py.html
index 29cfdf9..c2ffd1a 100644
--- a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_slice_py.html
+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_slice_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_snapshot_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_snapshot_py.html">&#xbb; next</a>
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_snapshot_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_snapshot_py.html
index 9439850..cd3fead 100644
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+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_snapshot_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
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@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_193cb9ad0ec3bf66_test_cpptraj_strip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_strip_py.html b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_strip_py.html
index 7c53337..951c3a8 100644
--- a/coverage/z_193cb9ad0ec3bf66_test_cpptraj_strip_py.html
+++ b/coverage/z_193cb9ad0ec3bf66_test_cpptraj_strip_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,7 +106,7 @@ <h2>
             <a class="nav" href="z_018feecd41fcf543_test_gmx_cluster_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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 </footer>
diff --git a/coverage/z_8185a593ca2a23a7___init___py.html b/coverage/z_8185a593ca2a23a7___init___py.html
index 19a0849..40bfdaa 100644
--- a/coverage/z_8185a593ca2a23a7___init___py.html
+++ b/coverage/z_8185a593ca2a23a7___init___py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -100,7 +100,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_8185a593ca2a23a7_common_py.html b/coverage/z_8185a593ca2a23a7_common_py.html
index b407601..521065b 100644
--- a/coverage/z_8185a593ca2a23a7_common_py.html
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@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -739,7 +739,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_8185a593ca2a23a7_gmx_cluster_py.html b/coverage/z_8185a593ca2a23a7_gmx_cluster_py.html
index ff2022a..eebd1bb 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_cluster_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_cluster_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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@@ -221,7 +221,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">fit_selection</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_selection</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.fit_selection} {self.output_selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">,</span> <span class="str">'cluster'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -320,7 +320,7 @@ <h2>
             <a class="nav" href="z_8185a593ca2a23a7_gmx_energy_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8185a593ca2a23a7_gmx_energy_py.html b/coverage/z_8185a593ca2a23a7_gmx_energy_py.html
index 9d823ae..7e4b16b 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_energy_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_energy_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8185a593ca2a23a7_gmx_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -329,7 +329,7 @@ <h2>
             <a class="nav" href="z_8185a593ca2a23a7_gmx_image_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8185a593ca2a23a7_gmx_image_py.html b/coverage/z_8185a593ca2a23a7_gmx_image_py.html
index 26bdec9..c62965d 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_image_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_image_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8185a593ca2a23a7_gmx_rgyr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -233,7 +233,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">selections</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{selections}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">,</span> <span class="str">'trjconv'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -321,7 +321,7 @@ <h2>
             <a class="nav" href="z_8185a593ca2a23a7_gmx_rgyr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8185a593ca2a23a7_gmx_rgyr_py.html b/coverage/z_8185a593ca2a23a7_gmx_rgyr_py.html
index ca23c35..caf3eb8 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_rgyr_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_rgyr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8185a593ca2a23a7_gmx_rms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -192,7 +192,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">selection</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">,</span> <span class="str">'gyrate'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -271,7 +271,7 @@ <h2>
             <a class="nav" href="z_8185a593ca2a23a7_gmx_rms_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8185a593ca2a23a7_gmx_rms_py.html b/coverage/z_8185a593ca2a23a7_gmx_rms_py.html
index 191775d..da926fe 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_rms_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_rms_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8185a593ca2a23a7_gmx_trjconv_str_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -192,7 +192,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">selection</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">selection</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.selection} {self.selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">,</span> <span class="str">'rms'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -271,7 +271,7 @@ <h2>
             <a class="nav" href="z_8185a593ca2a23a7_gmx_trjconv_str_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_ens_py.html b/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_ens_py.html
index a8c4fa7..e177cb3 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_ens_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_ens_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8185a593ca2a23a7_gmx_trjconv_trj_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">selection</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># if container execution, output to container_volume_path, else to unique_dir</span>&nbsp;</span><span class="r"></span></p>
@@ -313,7 +313,7 @@ <h2>
             <a class="nav" href="z_8185a593ca2a23a7_gmx_trjconv_trj_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_py.html b/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_py.html
index a4d3349..ead93db 100644
--- a/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_py.html
+++ b/coverage/z_8185a593ca2a23a7_gmx_trjconv_str_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8185a593ca2a23a7_gmx_trjconv_str_ens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -198,7 +198,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">selection</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
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-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="str">'''if not self.io_dict["in"]["input_index_path"]:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="str">'''if not self.io_dict["in"]["input_index_path"]:</span>&nbsp;</span><span class="r"></span></p>
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+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/coverage/z_c20cb7e24cb6893b___init___py.html b/coverage/z_c20cb7e24cb6893b___init___py.html
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-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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     </div>
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diff --git a/coverage/z_ffd130d3bf47de36___init___py.html b/coverage/z_ffd130d3bf47de36___init___py.html
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.10">coverage.py v7.6.10</a>,
-            created at 2025-01-08 09:43 +0000
+            created at 2025-01-08 09:46 +0000
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diff --git a/flake8/index.html b/flake8/index.html
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diff --git a/junit/junit.xml b/junit/junit.xml
index 6d6dd1f..4727e50 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
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\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index acdeed8..75788ba 100644
--- a/junit/report.html
+++ b/junit/report.html
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-    <p>Report generated on 08-Jan-2025 at 09:42:37 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 08-Jan-2025 at 09:46:27 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
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         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.12.8&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-204-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.4&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_average.py::TestCpptrajAverage::test_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_average.py::TestCpptrajAverage::test_average&#34;, &#34;duration&#34;: &#34;388 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_average.py::TestCpptrajAverage::test_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;388 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:50,145 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_average Version: 5.0.1\n2025-01-08 09:41:50,146 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb directory successfully created\n2025-01-08 09:41:50,149 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb\n2025-01-08 09:41:50,154 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb\n2025-01-08 09:41:50,155 [MainThread  ] [INFO ]  cpptraj -i c505871e-dfc7-4ef9-8491-c5e78898c22c/instructions.in\n\n2025-01-08 09:41:50,205 [MainThread  ] [INFO ]  Executing: cpptraj -i c505871e-dfc7-4ef9-8491-c5e78898c22c/instructions.in...\n2025-01-08 09:41:50,205 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:50,205 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:50\n| Available memory: 10.510 GB\n\nINPUT: Reading input from &amp;#x27;c505871e-dfc7-4ef9-8491-c5e78898c22c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb&amp;#x27; as PDB\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tWriting averaged coords to file &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb pdb]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6156.1192 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames,  &amp;#x27;output.pdb&amp;#x27; is a PDB file, Parm cpptraj.parm.top: Writing 1 frames (1-Last, 1)\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0081 s ( 79.55%)\nTIME:\t\tAction Post        : 0.0020 s ( 19.79%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.10%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0102 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0317 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:50,207 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb&amp;#x27;, &amp;#x27;c505871e-dfc7-4ef9-8491-c5e78898c22c&amp;#x27;]\n2025-01-08 09:41:50,208 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_average/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_6/cpptraj_average/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.average.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 710\n     Atoms ALIGNED in PDB_B: 710\n     RMS: 5.855159840099637e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_average Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:63 cpptraj -i c505871e-dfc7-4ef9-8491-c5e78898c22c/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i c505871e-dfc7-4ef9-8491-c5e78898c22c/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:50\n| Available memory: 10.510 GB\n\nINPUT: Reading input from &amp;#x27;c505871e-dfc7-4ef9-8491-c5e78898c22c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb&amp;#x27; as PDB\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tWriting averaged coords to file &amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average /tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb/output.pdb pdb]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6156.1192 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames,  &amp;#x27;output.pdb&amp;#x27; is a PDB file, Parm cpptraj.parm.top: Writing 1 frames (1-Last, 1)\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0081 s ( 79.55%)\nTIME:\t\tAction Post        : 0.0020 s ( 19.79%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.10%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0102 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0317 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_average/sandbox_268aa4f4-a11c-4416-bae6-1eaf6dc64bcb&amp;#x27;, &amp;#x27;c505871e-dfc7-4ef9-8491-c5e78898c22c&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_average/cpptraj_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorFirst::test_bfactor_first&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorFirst::test_bfactor_first&#34;, &#34;duration&#34;: &#34;260 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorFirst::test_bfactor_first&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;260 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:50,537 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\n2025-01-08 09:41:50,537 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3 directory successfully created\n2025-01-08 09:41:50,540 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3\n2025-01-08 09:41:50,545 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3\n2025-01-08 09:41:50,546 [MainThread  ] [INFO ]  cpptraj -i b1cde8ba-1b10-4a33-89f7-d00b392afd64/instructions.in\n\n2025-01-08 09:41:50,591 [MainThread  ] [INFO ]  Executing: cpptraj -i b1cde8ba-1b10-4a33-89f7-d00b392afd64/instructions.in...\n2025-01-08 09:41:50,591 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:50,591 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:50\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;b1cde8ba-1b10-4a33-89f7-d00b392afd64/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5877.5126 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0085 s ( 91.71%)\nTIME:\t\tAction Post        : 0.0001 s (  0.65%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0007 s (  7.29%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0093 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0288 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:50,594 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3&amp;#x27;, &amp;#x27;b1cde8ba-1b10-4a33-89f7-d00b392afd64&amp;#x27;]\n2025-01-08 09:41:50,594 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_bfactor_first/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_bfactor_first/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.first.dat\n        File_A hash: b&amp;quot;\\x83\\x86\\xed &amp;#x27;\\x03v\\x965\\x10\\xae!)\\x1f\\x8d\\xbat(  \\x92\\xb3w\\x08 \\xafjz\\n\\xf0\\x9b\\x02&amp;quot;\n        File_B hash: b&amp;quot;\\x83\\x86\\xed &amp;#x27;\\x03v\\x965\\x10\\xae!)\\x1f\\x8d\\xbat(  \\x92\\xb3w\\x08 \\xafjz\\n\\xf0\\x9b\\x02&amp;quot;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:63 cpptraj -i b1cde8ba-1b10-4a33-89f7-d00b392afd64/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:36 Executing: cpptraj -i b1cde8ba-1b10-4a33-89f7-d00b392afd64/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:50\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;b1cde8ba-1b10-4a33-89f7-d00b392afd64/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5877.5126 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0085 s ( 91.71%)\nTIME:\t\tAction Post        : 0.0001 s (  0.65%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0007 s (  7.29%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0093 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0288 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_first/sandbox_3c123f96-6759-4765-b4dc-a1a86dd1eca3&amp;#x27;, &amp;#x27;b1cde8ba-1b10-4a33-89f7-d00b392afd64&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorAverage::test_bfactor_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorAverage::test_bfactor_average&#34;, &#34;duration&#34;: &#34;283 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorAverage::test_bfactor_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;283 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:50,815 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\n2025-01-08 09:41:50,815 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b directory successfully created\n2025-01-08 09:41:50,819 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b\n2025-01-08 09:41:50,823 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b\n2025-01-08 09:41:50,824 [MainThread  ] [INFO ]  cpptraj -i 0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c/instructions.in\n\n2025-01-08 09:41:50,876 [MainThread  ] [INFO ]  Executing: cpptraj -i 0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c/instructions.in...\n2025-01-08 09:41:50,876 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:50,876 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:50\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6237.5250 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.09%)\nTIME:\t\tTrajectory Process : 0.0080 s ( 97.54%)\nTIME:\t\tAction Post        : 0.0001 s (  1.75%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.12%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0082 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/output.dat byres bfactor]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 8706.2511 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0057 s ( 80.83%)\nTIME:\t\tAction Post        : 0.0006 s (  8.75%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0007 s ( 10.23%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0071 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0349 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:50,878 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b&amp;#x27;, &amp;#x27;0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c&amp;#x27;]\n2025-01-08 09:41:50,878 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_bfactor_average/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_bfactor_average/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.average.dat\n        File_A hash: b&amp;#x27;\\x8d\\x1e\\xa1\\xbaL\\x95\\xf2\\x86\\x0eI\\xd0\\x06\\xff\\xb1\\xfe;\\xe8&amp;amp;^\\xf6\\x8f\\x00\\x18\\xab\\x1dy\\xacC:\\tR\\x16&amp;#x27;\n        File_B hash: b&amp;#x27;\\x8d\\x1e\\xa1\\xbaL\\x95\\xf2\\x86\\x0eI\\xd0\\x06\\xff\\xb1\\xfe;\\xe8&amp;amp;^\\xf6\\x8f\\x00\\x18\\xab\\x1dy\\xacC:\\tR\\x16&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:63 cpptraj -i 0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:50\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6237.5250 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.09%)\nTIME:\t\tTrajectory Process : 0.0080 s ( 97.54%)\nTIME:\t\tAction Post        : 0.0001 s (  1.75%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.12%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0082 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b/output.dat byres bfactor]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 8706.2511 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0057 s ( 80.83%)\nTIME:\t\tAction Post        : 0.0006 s (  8.75%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0007 s ( 10.23%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0071 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0349 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_average/sandbox_32398faa-9e36-4d49-90ce-14ae6455ac1b&amp;#x27;, &amp;#x27;0bd0a325-2dd9-4ee7-9f42-16aa6dfe723c&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorExperimental::test_bfactor_experimental&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorExperimental::test_bfactor_experimental&#34;, &#34;duration&#34;: &#34;272 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorExperimental::test_bfactor_experimental&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;272 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:51,081 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\n2025-01-08 09:41:51,082 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5 directory successfully created\n2025-01-08 09:41:51,085 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5\n2025-01-08 09:41:51,089 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5\n2025-01-08 09:41:51,090 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5\n2025-01-08 09:41:51,090 [MainThread  ] [INFO ]  cpptraj -i 055c5957-439e-4808-a912-cc8391cfb61d/instructions.in\n\n2025-01-08 09:41:51,149 [MainThread  ] [INFO ]  Executing: cpptraj -i 055c5957-439e-4808-a912-cc8391cfb61d/instructions.in...\n2025-01-08 09:41:51,149 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:51,150 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;055c5957-439e-4808-a912-cc8391cfb61d/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5880.2775 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.19%)\nTIME:\t\tTrajectory Process : 0.0085 s ( 91.18%)\nTIME:\t\tAction Post        : 0.0000 s (  0.32%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0007 s (  7.36%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0093 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0424 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:51,152 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5&amp;#x27;, &amp;#x27;055c5957-439e-4808-a912-cc8391cfb61d&amp;#x27;]\n2025-01-08 09:41:51,152 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.experimental.dat\n        File_A hash: b&amp;#x27;\\xa4\\xa2\\xa9\\xa9\\xfb+\\xf8X\\xf4\\x94\\xc4\\xbc\\x07\\x19\\x02J\\xd3\\xd7\\x9c\\xa7Ji\\xcc\\xf4[+\\x176\\xf8\\x98\\x94\\xa2&amp;#x27;\n        File_B hash: b&amp;#x27;\\xa4\\xa2\\xa9\\xa9\\xfb+\\xf8X\\xf4\\x94\\xc4\\xbc\\x07\\x19\\x02J\\xd3\\xd7\\x9c\\xa7Ji\\xcc\\xf4[+\\x176\\xf8\\x98\\x94\\xa2&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:63 cpptraj -i 055c5957-439e-4808-a912-cc8391cfb61d/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 055c5957-439e-4808-a912-cc8391cfb61d/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;055c5957-439e-4808-a912-cc8391cfb61d/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5880.2775 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.19%)\nTIME:\t\tTrajectory Process : 0.0085 s ( 91.18%)\nTIME:\t\tAction Post        : 0.0000 s (  0.32%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0007 s (  7.36%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0093 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0424 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_bfactor_experimental/sandbox_adf3debd-3583-4f46-8fc3-d9ab30a52da5&amp;#x27;, &amp;#x27;055c5957-439e-4808-a912-cc8391cfb61d&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_convert.py::TestCpptrajConvert::test_convert&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_convert.py::TestCpptrajConvert::test_convert&#34;, &#34;duration&#34;: &#34;254 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_convert.py::TestCpptrajConvert::test_convert&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;254 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:51,355 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_convert Version: 5.0.1\n2025-01-08 09:41:51,356 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8 directory successfully created\n2025-01-08 09:41:51,359 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8\n2025-01-08 09:41:51,363 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8\n2025-01-08 09:41:51,364 [MainThread  ] [INFO ]  cpptraj -i 99f70ebd-e7d1-4edc-92b1-71500e1b1452/instructions.in\n\n2025-01-08 09:41:51,405 [MainThread  ] [INFO ]  Executing: cpptraj -i 99f70ebd-e7d1-4edc-92b1-71500e1b1452/instructions.in...\n2025-01-08 09:41:51,405 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:51,405 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;99f70ebd-e7d1-4edc-92b1-71500e1b1452/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 9283.3271 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.13%)\nTIME:\t\tTrajectory Process : 0.0054 s ( 99.23%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0054 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0244 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:51,407 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8&amp;#x27;, &amp;#x27;99f70ebd-e7d1-4edc-92b1-71500e1b1452&amp;#x27;]\n2025-01-08 09:41:51,408 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_convert/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_convert/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.convert.netcdf\n     SIZE_A: 426420 bytes\n     SIZE_B: 426420 bytes\n     TOLERANCE: 1.0%, Low: 422155.8 bytes, High: 430684.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_convert Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:63 cpptraj -i 99f70ebd-e7d1-4edc-92b1-71500e1b1452/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 99f70ebd-e7d1-4edc-92b1-71500e1b1452/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;99f70ebd-e7d1-4edc-92b1-71500e1b1452/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 9283.3271 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.13%)\nTIME:\t\tTrajectory Process : 0.0054 s ( 99.23%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0054 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0244 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_convert/sandbox_12b9e95a-2df0-46eb-aefe-480de63d51a8&amp;#x27;, &amp;#x27;99f70ebd-e7d1-4edc-92b1-71500e1b1452&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_dry.py::TestCpptrajDry::test_dry&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_dry.py::TestCpptrajDry::test_dry&#34;, &#34;duration&#34;: &#34;270 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_dry.py::TestCpptrajDry::test_dry&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;270 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:51,613 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_dry Version: 5.0.1\n2025-01-08 09:41:51,613 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e directory successfully created\n2025-01-08 09:41:51,617 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e\n2025-01-08 09:41:51,622 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e\n2025-01-08 09:41:51,622 [MainThread  ] [INFO ]  cpptraj -i 85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9/instructions.in\n\n2025-01-08 09:41:51,674 [MainThread  ] [INFO ]  Executing: cpptraj -i 85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9/instructions.in...\n2025-01-08 09:41:51,675 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:51,675 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@H*,1H*,2H*,3H*]\n    STRIP: Stripping atoms in mask [!@H*,1H*,2H*,3H*]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (3 actions):\n  0: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  1: [strip !@H*,1H*,2H*,3H*]\n\tStripping 5698 atoms.\n\tStripped topology: 5509 atoms, 710 res, box: None, 5509 mol\n  2: [strip !@CA]\nWarning: Mask [!@CA] would strip all atoms. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 3427.9446 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0146 s ( 98.89%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0002 s (  0.01%)\nTIME:\tRun Total 0.0147 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0349 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:51,679 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e&amp;#x27;, &amp;#x27;85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9&amp;#x27;]\n2025-01-08 09:41:51,679 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_dry/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_dry/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.dry.netcdf\n     SIZE_A: 3305820 bytes\n     SIZE_B: 3305820 bytes\n     TOLERANCE: 1.0%, Low: 3272761.8 bytes, High: 3338878.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_dry Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:63 cpptraj -i 85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@H*,1H*,2H*,3H*]\n    STRIP: Stripping atoms in mask [!@H*,1H*,2H*,3H*]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (3 actions):\n  0: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  1: [strip !@H*,1H*,2H*,3H*]\n\tStripping 5698 atoms.\n\tStripped topology: 5509 atoms, 710 res, box: None, 5509 mol\n  2: [strip !@CA]\nWarning: Mask [!@CA] would strip all atoms. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 3427.9446 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0146 s ( 98.89%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0002 s (  0.01%)\nTIME:\tRun Total 0.0147 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0349 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_dry/sandbox_15e4d4c4-87c9-4bca-a0bb-b299e3606d1e&amp;#x27;, &amp;#x27;85b4ac84-07cb-4a8f-aa2c-f4d67cf292c9&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_image.py::TestCpptrajImage::test_image&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_image.py::TestCpptrajImage::test_image&#34;, &#34;duration&#34;: &#34;285 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_image.py::TestCpptrajImage::test_image&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;285 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:51,907 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_image Version: 5.0.1\n2025-01-08 09:41:51,907 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22 directory successfully created\n2025-01-08 09:41:51,910 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22\n2025-01-08 09:41:51,915 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22\n2025-01-08 09:41:51,915 [MainThread  ] [INFO ]  cpptraj -i c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91/instructions.in\n\n2025-01-08 09:41:51,963 [MainThread  ] [INFO ]  Executing: cpptraj -i c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91/instructions.in...\n2025-01-08 09:41:51,963 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:51,964 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (4 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 4436.9509 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0113 s ( 99.52%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.08%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0113 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0309 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:51,966 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22&amp;#x27;, &amp;#x27;c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91&amp;#x27;]\n2025-01-08 09:41:51,966 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_image/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_image/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.image.netcdf\n     SIZE_A: 426420 bytes\n     SIZE_B: 426420 bytes\n     TOLERANCE: 1.0%, Low: 422155.8 bytes, High: 430684.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_image Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:63 cpptraj -i c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:36 Executing: cpptraj -i c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:51\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (4 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 4436.9509 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0113 s ( 99.52%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.08%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0113 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0309 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_image/sandbox_fb21de53-b758-40ab-a26a-3b40c900cb22&amp;#x27;, &amp;#x27;c1a8c284-7ac3-4c84-9ad8-8e2dd8b03d91&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_image/cpptraj_image_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_input.py::TestCpptrajInput::test_input&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_input.py::TestCpptrajInput::test_input&#34;, &#34;duration&#34;: &#34;262 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_input.py::TestCpptrajInput::test_input&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;262 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:52,174 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_input Version: 5.0.1\n2025-01-08 09:41:52,174 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_input/sandbox_741a965b-91ef-4bca-8ba0-efdc58683b94 directory successfully created\n2025-01-08 09:41:52,175 [MainThread  ] [INFO ]  cpptraj -i cpptraj_input_instructions.in\n\n2025-01-08 09:41:52,229 [MainThread  ] [INFO ]  Executing: cpptraj -i cpptraj_input_instructions.in...\n2025-01-08 09:41:52,229 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:52,229 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.517 GB\n\nINPUT: Reading input from &amp;#x27;cpptraj_input_instructions.in&amp;#x27;\n  [parm /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top]\n\tReading &amp;#x27;/home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd]\n\tReading &amp;#x27;/home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [trajout /tmp/biobb/unitests_6/cpptraj_input/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_input/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_input/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2745.7441 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.04%)\nTIME:\t\tTrajectory Process : 0.0182 s ( 99.87%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0182 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0378 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_input/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_input/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.in.netcdf\n     SIZE_A: 6724620 bytes\n     SIZE_B: 6724620 bytes\n     TOLERANCE: 1.0%, Low: 6657373.8 bytes, High: 6791866.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_input/cpptraj_input_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_input Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_input/cpptraj_input_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_input/sandbox_741a965b-91ef-4bca-8ba0-efdc58683b94 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:63 cpptraj -i cpptraj_input_instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:36 Executing: cpptraj -i cpptraj_input_instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.517 GB\n\nINPUT: Reading input from &amp;#x27;cpptraj_input_instructions.in&amp;#x27;\n  [parm /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top]\n\tReading &amp;#x27;/home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd]\n\tReading &amp;#x27;/home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [trajout /tmp/biobb/unitests_6/cpptraj_input/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_input/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_input/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2745.7441 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.04%)\nTIME:\t\tTrajectory Process : 0.0182 s ( 99.87%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0182 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0378 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_mask.py::TestCpptrajMask::test_mask&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_mask.py::TestCpptrajMask::test_mask&#34;, &#34;duration&#34;: &#34;260 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_mask.py::TestCpptrajMask::test_mask&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;260 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:52,440 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_mask Version: 5.0.1\n2025-01-08 09:41:52,440 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe directory successfully created\n2025-01-08 09:41:52,443 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe\n2025-01-08 09:41:52,447 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe\n2025-01-08 09:41:52,447 [MainThread  ] [INFO ]  cpptraj -i 42387cc3-7793-4b71-9779-e1f9a5ae0b46/instructions.in\n\n2025-01-08 09:41:52,489 [MainThread  ] [INFO ]  Executing: cpptraj -i 42387cc3-7793-4b71-9779-e1f9a5ae0b46/instructions.in...\n2025-01-08 09:41:52,489 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:52,490 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;42387cc3-7793-4b71-9779-e1f9a5ae0b46/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 9092.5623 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.16%)\nTIME:\t\tTrajectory Process : 0.0055 s ( 99.24%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0055 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0250 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:52,492 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe&amp;#x27;, &amp;#x27;42387cc3-7793-4b71-9779-e1f9a5ae0b46&amp;#x27;]\n2025-01-08 09:41:52,492 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_mask/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_mask/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.mask.netcdf\n     SIZE_A: 426420 bytes\n     SIZE_B: 426420 bytes\n     TOLERANCE: 1.0%, Low: 422155.8 bytes, High: 430684.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_mask Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:63 cpptraj -i 42387cc3-7793-4b71-9779-e1f9a5ae0b46/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 42387cc3-7793-4b71-9779-e1f9a5ae0b46/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;42387cc3-7793-4b71-9779-e1f9a5ae0b46/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 9092.5623 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.16%)\nTIME:\t\tTrajectory Process : 0.0055 s ( 99.24%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0055 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0250 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_mask/sandbox_1899f0d6-f09e-456a-901f-7370fc255bbe&amp;#x27;, &amp;#x27;42387cc3-7793-4b71-9779-e1f9a5ae0b46&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rgyr.py::TestCpptrajRgyr::test_rgyr&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rgyr.py::TestCpptrajRgyr::test_rgyr&#34;, &#34;duration&#34;: &#34;258 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rgyr.py::TestCpptrajRgyr::test_rgyr&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;258 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:52,698 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rgyr Version: 5.0.1\n2025-01-08 09:41:52,698 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3 directory successfully created\n2025-01-08 09:41:52,701 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3\n2025-01-08 09:41:52,705 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3\n2025-01-08 09:41:52,706 [MainThread  ] [INFO ]  cpptraj -i 6bb8b166-5122-4791-8c19-0cadc067ba38/instructions.in\n\n2025-01-08 09:41:52,750 [MainThread  ] [INFO ]  Executing: cpptraj -i 6bb8b166-5122-4791-8c19-0cadc067ba38/instructions.in...\n2025-01-08 09:41:52,750 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:52,750 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;6bb8b166-5122-4791-8c19-0cadc067ba38/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [radgyr time 1 out /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/output.dat]\n    RADGYR: Calculating for atoms in mask *.\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [radgyr time 1 out /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/output.dat]\n\t* (710 atoms).\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6239.0816 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRoG_00002 &amp;quot;RoG_00002&amp;quot; (double), size is 50 (0.400 kB)\n\tRoG_00002[Max] &amp;quot;RoG_00002[Max]&amp;quot; (double), size is 50 (0.400 kB)\n    Total data set memory usage is at least 1.200 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RoG_00002 RoG_00002[Max]\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.09%)\nTIME:\t\tTrajectory Process : 0.0080 s ( 97.87%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  1.71%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0082 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0276 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:52,752 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3&amp;#x27;, &amp;#x27;6bb8b166-5122-4791-8c19-0cadc067ba38&amp;#x27;]\n2025-01-08 09:41:52,752 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rgyr/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rgyr/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat\n        File_A hash: b&amp;#x27;\\t\\xc9\\xcd\\xa6\\xf1l\\xdf\\x18\\xe3\\x8b\\x81\\x07\\x08\\x16d#S*\\xa6DF\\x94\\x1b^\\xfcz\\xeb\\xfe]\\xf5c5&amp;#x27;\n        File_B hash: b&amp;#x27;\\t\\xc9\\xcd\\xa6\\xf1l\\xdf\\x18\\xe3\\x8b\\x81\\x07\\x08\\x16d#S*\\xa6DF\\x94\\x1b^\\xfcz\\xeb\\xfe]\\xf5c5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rgyr Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:63 cpptraj -i 6bb8b166-5122-4791-8c19-0cadc067ba38/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 6bb8b166-5122-4791-8c19-0cadc067ba38/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;6bb8b166-5122-4791-8c19-0cadc067ba38/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [radgyr time 1 out /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/output.dat]\n    RADGYR: Calculating for atoms in mask *.\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [radgyr time 1 out /tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3/output.dat]\n\t* (710 atoms).\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6239.0816 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRoG_00002 &amp;quot;RoG_00002&amp;quot; (double), size is 50 (0.400 kB)\n\tRoG_00002[Max] &amp;quot;RoG_00002[Max]&amp;quot; (double), size is 50 (0.400 kB)\n    Total data set memory usage is at least 1.200 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RoG_00002 RoG_00002[Max]\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.09%)\nTIME:\t\tTrajectory Process : 0.0080 s ( 97.87%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  1.71%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0082 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0276 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rgyr/sandbox_497f089a-f8fc-4d4a-97ee-586ed018eff3&amp;#x27;, &amp;#x27;6bb8b166-5122-4791-8c19-0cadc067ba38&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsFirst::test_rms_first&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsFirst::test_rms_first&#34;, &#34;duration&#34;: &#34;298 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsFirst::test_rms_first&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;298 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:52,958 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\n2025-01-08 09:41:52,959 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b directory successfully created\n2025-01-08 09:41:52,962 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b\n2025-01-08 09:41:52,966 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b\n2025-01-08 09:41:52,966 [MainThread  ] [INFO ]  cpptraj -i 374ca570-ad43-4735-87c8-cbed55767447/instructions.in\n\n2025-01-08 09:41:53,048 [MainThread  ] [INFO ]  Executing: cpptraj -i 374ca570-ad43-4735-87c8-cbed55767447/instructions.in...\n2025-01-08 09:41:53,048 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:53,048 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;374ca570-ad43-4735-87c8-cbed55767447/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first out /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.dat]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first out /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.dat]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 1083.2828 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00002\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.02%)\nTIME:\t\tTrajectory Process : 0.0462 s ( 99.72%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  0.19%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0463 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0656 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:53,051 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b&amp;#x27;, &amp;#x27;374ca570-ad43-4735-87c8-cbed55767447&amp;#x27;]\n2025-01-08 09:41:53,052 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rms_first/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rms_first/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.dat\n        File_A hash: b&amp;#x27;b\\x15\\x8a\\x17\\xa1\\\\\\xb7{\\x98\\xfc\\x8dx\\xc5Sz)4P\\xe0D\\xee@\\xc3rQ\\xf26n\\x99\\xe1\\\\=&amp;#x27;\n        File_B hash: b&amp;#x27;b\\x15\\x8a\\x17\\xa1\\\\\\xb7{\\x98\\xfc\\x8dx\\xc5Sz)4P\\xe0D\\xee@\\xc3rQ\\xf26n\\x99\\xe1\\\\=&amp;#x27;\nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rms_first/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_rms_first/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.netcdf\n     SIZE_A: 862731 bytes\n     SIZE_B: 862731 bytes\n     TOLERANCE: 1.0%, Low: 854103.69 bytes, High: 871358.31 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:63 cpptraj -i 374ca570-ad43-4735-87c8-cbed55767447/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 374ca570-ad43-4735-87c8-cbed55767447/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:52\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;374ca570-ad43-4735-87c8-cbed55767447/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first out /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.dat]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first out /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.dat]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 1083.2828 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00002\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.02%)\nTIME:\t\tTrajectory Process : 0.0462 s ( 99.72%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  0.19%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0463 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0656 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_first/sandbox_7a02a03a-17b3-44af-9d79-071ebe9ec32b&amp;#x27;, &amp;#x27;374ca570-ad43-4735-87c8-cbed55767447&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsAverage::test_rms_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsAverage::test_rms_average&#34;, &#34;duration&#34;: &#34;845 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsAverage::test_rms_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;845 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:53,256 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\n2025-01-08 09:41:53,256 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1 directory successfully created\n2025-01-08 09:41:53,259 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1\n2025-01-08 09:41:53,264 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1\n2025-01-08 09:41:53,264 [MainThread  ] [INFO ]  cpptraj -i b956f6b5-02c9-44a3-a9f0-a586e4937c16/instructions.in\n\n2025-01-08 09:41:53,884 [MainThread  ] [INFO ]  Executing: cpptraj -i b956f6b5-02c9-44a3-a9f0-a586e4937c16/instructions.in...\n2025-01-08 09:41:53,884 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:53,885 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:53\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;b956f6b5-02c9-44a3-a9f0-a586e4937c16/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6215.0404 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0080 s ( 97.72%)\nTIME:\t\tAction Post        : 0.0001 s (  1.59%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.11%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0082 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA out /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.dat]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [rms ref MyAvg @CA out /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 87.8884 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00003\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.00%)\nTIME:\t\tTrajectory Process : 0.5689 s ( 99.98%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  0.02%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.5690 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.5964 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:53,896 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1&amp;#x27;, &amp;#x27;b956f6b5-02c9-44a3-a9f0-a586e4937c16&amp;#x27;]\n2025-01-08 09:41:53,896 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rms_average/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rms_average/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.average.dat\n        File_A hash: b&amp;#x27;\\xd9\\xbf\\x08bIk\\xd1\\x89X\\xec\\x95#&amp;quot;\\xda\\xb6\\xf1\\xb9\\xd4\\\\\\x80\\xfe\\xaef\\x16\\xf85\\x9f(\\x8a\\xa3\\xbbQ&amp;#x27;\n        File_B hash: b&amp;#x27;\\xd9\\xbf\\x08bIk\\xd1\\x89X\\xec\\x95#&amp;quot;\\xda\\xb6\\xf1\\xb9\\xd4\\\\\\x80\\xfe\\xaef\\x16\\xf85\\x9f(\\x8a\\xa3\\xbbQ&amp;#x27;\nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rms_average/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_rms_average/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.average.netcdf\n     SIZE_A: 13616631 bytes\n     SIZE_B: 13616631 bytes\n     TOLERANCE: 1.0%, Low: 13480464.69 bytes, High: 13752797.31 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:63 cpptraj -i b956f6b5-02c9-44a3-a9f0-a586e4937c16/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i b956f6b5-02c9-44a3-a9f0-a586e4937c16/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:53\n| Available memory: 10.507 GB\n\nINPUT: Reading input from &amp;#x27;b956f6b5-02c9-44a3-a9f0-a586e4937c16/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6215.0404 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0080 s ( 97.72%)\nTIME:\t\tAction Post        : 0.0001 s (  1.59%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.11%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0082 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA out /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.dat]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [rms ref MyAvg @CA out /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 87.8884 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00003\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.00%)\nTIME:\t\tTrajectory Process : 0.5689 s ( 99.98%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  0.02%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.5690 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.5964 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_average/sandbox_f30c61c6-43f4-4d30-a576-e2ab080dcee1&amp;#x27;, &amp;#x27;b956f6b5-02c9-44a3-a9f0-a586e4937c16&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsExperimental::test_rms_experimental&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsExperimental::test_rms_experimental&#34;, &#34;duration&#34;: &#34;327 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsExperimental::test_rms_experimental&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;327 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:54,105 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\n2025-01-08 09:41:54,105 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d directory successfully created\n2025-01-08 09:41:54,109 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d\n2025-01-08 09:41:54,113 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d\n2025-01-08 09:41:54,114 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d\n2025-01-08 09:41:54,115 [MainThread  ] [INFO ]  cpptraj -i 064178d1-c405-479c-ae5b-e3da35ed1257/instructions.in\n\n2025-01-08 09:41:54,222 [MainThread  ] [INFO ]  Executing: cpptraj -i 064178d1-c405-479c-ae5b-e3da35ed1257/instructions.in...\n2025-01-08 09:41:54,223 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:54,223 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;064178d1-c405-479c-ae5b-e3da35ed1257/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA out /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.dat]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA out /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 911.1285 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00004\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0549 s ( 99.58%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  0.17%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0551 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0900 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:54,226 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d&amp;#x27;, &amp;#x27;064178d1-c405-479c-ae5b-e3da35ed1257&amp;#x27;]\n2025-01-08 09:41:54,226 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rms_experimental/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rms_experimental/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.experimental.dat\n        File_A hash: b&amp;#x27;\\x84\\xe9\\x89\\xf1!\\xb6e\\x9d\\x8b\\x15\\n\\xe5y\\x0f\\x01Hv3\\xe6\\x90\\x8e\\xe2|\\xc4:4\\xd7\\xf8\\xc0\\x06\\xc8m&amp;#x27;\n        File_B hash: b&amp;#x27;\\x84\\xe9\\x89\\xf1!\\xb6e\\x9d\\x8b\\x15\\n\\xe5y\\x0f\\x01Hv3\\xe6\\x90\\x8e\\xe2|\\xc4:4\\xd7\\xf8\\xc0\\x06\\xc8m&amp;#x27;\nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rms_experimental/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_rms_experimental/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.experimental.netcdf\n     SIZE_A: 862731 bytes\n     SIZE_B: 862731 bytes\n     TOLERANCE: 1.0%, Low: 854103.69 bytes, High: 871358.31 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:63 cpptraj -i 064178d1-c405-479c-ae5b-e3da35ed1257/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 064178d1-c405-479c-ae5b-e3da35ed1257/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;064178d1-c405-479c-ae5b-e3da35ed1257/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA out /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.dat]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA out /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 911.1285 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00004\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0549 s ( 99.58%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0001 s (  0.17%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0551 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0900 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rms_experimental/sandbox_da213cdf-2229-4e0a-992b-cc76d4fe3c5d&amp;#x27;, &amp;#x27;064178d1-c405-479c-ae5b-e3da35ed1257&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfFirst::test_rmsf_first&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfFirst::test_rmsf_first&#34;, &#34;duration&#34;: &#34;261 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfFirst::test_rmsf_first&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;261 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:54,433 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\n2025-01-08 09:41:54,433 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8 directory successfully created\n2025-01-08 09:41:54,437 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8\n2025-01-08 09:41:54,441 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8\n2025-01-08 09:41:54,442 [MainThread  ] [INFO ]  cpptraj -i 056a7d15-19e8-4674-81f7-ce95d33b8a0a/instructions.in\n\n2025-01-08 09:41:54,487 [MainThread  ] [INFO ]  Executing: cpptraj -i 056a7d15-19e8-4674-81f7-ce95d33b8a0a/instructions.in...\n2025-01-08 09:41:54,487 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:54,487 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.505 GB\n\nINPUT: Reading input from &amp;#x27;056a7d15-19e8-4674-81f7-ce95d33b8a0a/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5796.4294 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0086 s ( 93.03%)\nTIME:\t\tAction Post        : 0.0001 s (  0.61%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0006 s (  6.03%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0093 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0276 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:54,489 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8&amp;#x27;, &amp;#x27;056a7d15-19e8-4674-81f7-ce95d33b8a0a&amp;#x27;]\n2025-01-08 09:41:54,489 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rmsf_first/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rmsf_first/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.first.dat\n        File_A hash: b&amp;#x27;\\xe2\\xb6\\x11\\xbc\\xc7\\x9dl\\xb4_\\xb8\\x8e\\x1e^0U\\x00U\\xdaf\\x90\\xac\\xf6\\xd1:\\x0c\\x0c\\xac\\x02m\\xf2\\x01\\t&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe2\\xb6\\x11\\xbc\\xc7\\x9dl\\xb4_\\xb8\\x8e\\x1e^0U\\x00U\\xdaf\\x90\\xac\\xf6\\xd1:\\x0c\\x0c\\xac\\x02m\\xf2\\x01\\t&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:63 cpptraj -i 056a7d15-19e8-4674-81f7-ce95d33b8a0a/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 056a7d15-19e8-4674-81f7-ce95d33b8a0a/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.505 GB\n\nINPUT: Reading input from &amp;#x27;056a7d15-19e8-4674-81f7-ce95d33b8a0a/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5796.4294 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0086 s ( 93.03%)\nTIME:\t\tAction Post        : 0.0001 s (  0.61%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0006 s (  6.03%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0093 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0276 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_first/sandbox_5b0f1431-a68b-4df4-bfa1-7ad930e241d8&amp;#x27;, &amp;#x27;056a7d15-19e8-4674-81f7-ce95d33b8a0a&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfAverage::test_rmsf_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfAverage::test_rmsf_average&#34;, &#34;duration&#34;: &#34;269 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfAverage::test_rmsf_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;269 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:54,695 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\n2025-01-08 09:41:54,696 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b directory successfully created\n2025-01-08 09:41:54,699 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b\n2025-01-08 09:41:54,704 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b\n2025-01-08 09:41:54,705 [MainThread  ] [INFO ]  cpptraj -i 3ac23f12-e5df-4773-b594-7dd547d1240c/instructions.in\n\n2025-01-08 09:41:54,757 [MainThread  ] [INFO ]  Executing: cpptraj -i 3ac23f12-e5df-4773-b594-7dd547d1240c/instructions.in...\n2025-01-08 09:41:54,757 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:54,758 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;3ac23f12-e5df-4773-b594-7dd547d1240c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6158.3939 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.08%)\nTIME:\t\tTrajectory Process : 0.0081 s ( 97.42%)\nTIME:\t\tAction Post        : 0.0002 s (  1.87%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.12%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0083 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/output.dat byres]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 9175.9956 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0054 s ( 80.85%)\nTIME:\t\tAction Post        : 0.0007 s (  9.75%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0006 s (  9.23%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0067 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0349 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:54,759 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b&amp;#x27;, &amp;#x27;3ac23f12-e5df-4773-b594-7dd547d1240c&amp;#x27;]\n2025-01-08 09:41:54,760 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rmsf_average/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rmsf_average/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.average.dat\n        File_A hash: b&amp;#x27;\\x0f\\xef\\x87\\xe6\\x0c\\xed\\xf4s\\xdf\\xf50\\x01X;\\xab@\\xcb\\xcd\\xb6\\xf5R\\x9b\\xdaI\\x85\\xb2\\xae\\xa5\\x9c\\xe1\\xe5\\xfc&amp;#x27;\n        File_B hash: b&amp;#x27;\\x0f\\xef\\x87\\xe6\\x0c\\xed\\xf4s\\xdf\\xf50\\x01X;\\xab@\\xcb\\xcd\\xb6\\xf5R\\x9b\\xdaI\\x85\\xb2\\xae\\xa5\\x9c\\xe1\\xe5\\xfc&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:63 cpptraj -i 3ac23f12-e5df-4773-b594-7dd547d1240c/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 3ac23f12-e5df-4773-b594-7dd547d1240c/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;3ac23f12-e5df-4773-b594-7dd547d1240c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 6158.3939 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.08%)\nTIME:\t\tTrajectory Process : 0.0081 s ( 97.42%)\nTIME:\t\tAction Post        : 0.0002 s (  1.87%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.12%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0083 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b/output.dat byres]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 9175.9956 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0054 s ( 80.85%)\nTIME:\t\tAction Post        : 0.0007 s (  9.75%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0006 s (  9.23%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0067 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0349 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_average/sandbox_d195c5f4-771d-490f-be3a-be9d6aded81b&amp;#x27;, &amp;#x27;3ac23f12-e5df-4773-b594-7dd547d1240c&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfExperimental::test_rmsf_experimental&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfExperimental::test_rmsf_experimental&#34;, &#34;duration&#34;: &#34;272 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfExperimental::test_rmsf_experimental&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;272 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:54,962 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\n2025-01-08 09:41:54,963 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820 directory successfully created\n2025-01-08 09:41:54,966 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820\n2025-01-08 09:41:54,970 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820\n2025-01-08 09:41:54,970 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820\n2025-01-08 09:41:54,971 [MainThread  ] [INFO ]  cpptraj -i 3e50fd2e-7a94-469f-9a9d-f60e0d445231/instructions.in\n\n2025-01-08 09:41:55,031 [MainThread  ] [INFO ]  Executing: cpptraj -i 3e50fd2e-7a94-469f-9a9d-f60e0d445231/instructions.in...\n2025-01-08 09:41:55,031 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:55,031 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.505 GB\n\nINPUT: Reading input from &amp;#x27;3e50fd2e-7a94-469f-9a9d-f60e0d445231/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5887.2012 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.20%)\nTIME:\t\tTrajectory Process : 0.0085 s ( 92.47%)\nTIME:\t\tAction Post        : 0.0000 s (  0.36%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0006 s (  6.71%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0092 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0429 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:55,033 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820&amp;#x27;, &amp;#x27;3e50fd2e-7a94-469f-9a9d-f60e0d445231&amp;#x27;]\n2025-01-08 09:41:55,033 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.experimental.dat\n        File_A hash: b&amp;#x27;\\xcb1@\\xbf\\x15I\\xb7xM{\\x85\\x03\\xbc\\xd4\\xfd\\xde\\x11\\x8d\\x1c\\xffj\\xe3]\\xb5!\\xb6C\\x7fMV\\xa0\\xc6&amp;#x27;\n        File_B hash: b&amp;#x27;\\xcb1@\\xbf\\x15I\\xb7xM{\\x85\\x03\\xbc\\xd4\\xfd\\xde\\x11\\x8d\\x1c\\xffj\\xe3]\\xb5!\\xb6C\\x7fMV\\xa0\\xc6&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:63 cpptraj -i 3e50fd2e-7a94-469f-9a9d-f60e0d445231/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 3e50fd2e-7a94-469f-9a9d-f60e0d445231/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:54\n| Available memory: 10.505 GB\n\nINPUT: Reading input from &amp;#x27;3e50fd2e-7a94-469f-9a9d-f60e0d445231/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 5887.2012 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.20%)\nTIME:\t\tTrajectory Process : 0.0085 s ( 92.47%)\nTIME:\t\tAction Post        : 0.0000 s (  0.36%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0006 s (  6.71%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0092 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0429 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_rmsf_experimental/sandbox_0ec5d380-f22e-41b6-bbd2-1328d5473820&amp;#x27;, &amp;#x27;3e50fd2e-7a94-469f-9a9d-f60e0d445231&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_slice.py::TestCpptrajSlice::test_slice&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_slice.py::TestCpptrajSlice::test_slice&#34;, &#34;duration&#34;: &#34;251 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_slice.py::TestCpptrajSlice::test_slice&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;251 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:55,237 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_slice Version: 5.0.1\n2025-01-08 09:41:55,237 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1 directory successfully created\n2025-01-08 09:41:55,240 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1\n2025-01-08 09:41:55,245 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1\n2025-01-08 09:41:55,245 [MainThread  ] [INFO ]  cpptraj -i c88abea4-dcb7-4c89-b627-42a69ca22b9d/instructions.in\n\n2025-01-08 09:41:55,284 [MainThread  ] [INFO ]  Executing: cpptraj -i c88abea4-dcb7-4c89-b627-42a69ca22b9d/instructions.in...\n2025-01-08 09:41:55,284 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:55,284 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:55\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;c88abea4-dcb7-4c89-b627-42a69ca22b9d/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.traj.dcd 2 20 2]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 10 of 50)\n  Coordinate processing will occur on 10 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (10 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (2-20, 2) -----\n 0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.\n\nRead 10 frames and processed 10 frames.\nTIME: Avg. throughput= 3176.6201 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.22%)\nTIME:\t\tTrajectory Process : 0.0031 s ( 98.78%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.03%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0032 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0223 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:55,286 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1&amp;#x27;, &amp;#x27;c88abea4-dcb7-4c89-b627-42a69ca22b9d&amp;#x27;]\n2025-01-08 09:41:55,286 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_slice/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_slice/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.slice.netcdf\n     SIZE_A: 85620 bytes\n     SIZE_B: 85620 bytes\n     TOLERANCE: 1.0%, Low: 84763.8 bytes, High: 86476.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_slice Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:63 cpptraj -i c88abea4-dcb7-4c89-b627-42a69ca22b9d/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:36 Executing: cpptraj -i c88abea4-dcb7-4c89-b627-42a69ca22b9d/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:55\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;c88abea4-dcb7-4c89-b627-42a69ca22b9d/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.traj.dcd 2 20 2]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 10 of 50)\n  Coordinate processing will occur on 10 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (10 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (2-20, 2) -----\n 0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.\n\nRead 10 frames and processed 10 frames.\nTIME: Avg. throughput= 3176.6201 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.22%)\nTIME:\t\tTrajectory Process : 0.0031 s ( 98.78%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.03%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0032 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0223 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_slice/sandbox_231fc3eb-7ace-418a-ab1d-a50522aad9b1&amp;#x27;, &amp;#x27;c88abea4-dcb7-4c89-b627-42a69ca22b9d&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_snapshot.py::TestCpptrajSnapshot::test_snapshot&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_snapshot.py::TestCpptrajSnapshot::test_snapshot&#34;, &#34;duration&#34;: &#34;362 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_snapshot.py::TestCpptrajSnapshot::test_snapshot&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;362 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:55,490 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_snapshot Version: 5.0.1\n2025-01-08 09:41:55,490 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e directory successfully created\n2025-01-08 09:41:55,493 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e\n2025-01-08 09:41:55,497 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e\n2025-01-08 09:41:55,498 [MainThread  ] [INFO ]  cpptraj -i dd8b290e-b169-47a0-89ae-a65090b5f0e4/instructions.in\n\n2025-01-08 09:41:55,535 [MainThread  ] [INFO ]  Executing: cpptraj -i dd8b290e-b169-47a0-89ae-a65090b5f0e4/instructions.in...\n2025-01-08 09:41:55,535 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:55,535 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:55\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;dd8b290e-b169-47a0-89ae-a65090b5f0e4/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.traj.dcd 12 12 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/output.pdb&amp;#x27; as PDB\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 1 of 50)\n  Coordinate processing will occur on 1 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.pdb&amp;#x27; (1 frames) is a PDB file\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/output.pdb (coordinates)\n----- cpptraj.traj.dcd (12-12, 1) -----\n100% Complete.\n\nRead 1 frames and processed 1 frames.\nTIME: Avg. throughput= 350.3854 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.24%)\nTIME:\t\tTrajectory Process : 0.0029 s ( 98.72%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0029 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0219 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:55,537 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e&amp;#x27;, &amp;#x27;dd8b290e-b169-47a0-89ae-a65090b5f0e4&amp;#x27;]\n2025-01-08 09:41:55,538 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_snapshot/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_6/cpptraj_snapshot/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.snapshot.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 710\n     Atoms ALIGNED in PDB_B: 710\n     RMS: 1.2327888345944396e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_snapshot Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:63 cpptraj -i dd8b290e-b169-47a0-89ae-a65090b5f0e4/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:36 Executing: cpptraj -i dd8b290e-b169-47a0-89ae-a65090b5f0e4/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:55\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;dd8b290e-b169-47a0-89ae-a65090b5f0e4/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.traj.dcd 12 12 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/output.pdb&amp;#x27; as PDB\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 1 of 50)\n  Coordinate processing will occur on 1 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.pdb&amp;#x27; (1 frames) is a PDB file\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e/output.pdb (coordinates)\n----- cpptraj.traj.dcd (12-12, 1) -----\n100% Complete.\n\nRead 1 frames and processed 1 frames.\nTIME: Avg. throughput= 350.3854 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.24%)\nTIME:\t\tTrajectory Process : 0.0029 s ( 98.72%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0000 s (  0.01%)\nTIME:\tRun Total 0.0029 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0219 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_snapshot/sandbox_5d4c00d2-35e4-4654-82c3-ae23256fec9e&amp;#x27;, &amp;#x27;dd8b290e-b169-47a0-89ae-a65090b5f0e4&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_strip.py::TestCpptrajStrip::test_strip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_strip.py::TestCpptrajStrip::test_strip&#34;, &#34;duration&#34;: &#34;279 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_strip.py::TestCpptrajStrip::test_strip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;279 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:55,853 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_strip Version: 5.0.1\n2025-01-08 09:41:55,854 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704 directory successfully created\n2025-01-08 09:41:55,857 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704\n2025-01-08 09:41:55,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704\n2025-01-08 09:41:55,862 [MainThread  ] [INFO ]  cpptraj -i 1640baa8-32bc-462c-86b7-721997822f47/instructions.in\n\n2025-01-08 09:41:55,923 [MainThread  ] [INFO ]  Executing: cpptraj -i 1640baa8-32bc-462c-86b7-721997822f47/instructions.in...\n2025-01-08 09:41:55,924 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:55,924 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:55\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;1640baa8-32bc-462c-86b7-721997822f47/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip @CA]\n    STRIP: Stripping atoms in mask [@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip @CA]\n\tStripping 710 atoms.\n\tStripped topology: 10497 atoms, 710 res, box: None, 2100 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2190.1007 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.03%)\nTIME:\t\tTrajectory Process : 0.0228 s ( 98.46%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0003 s (  0.02%)\nTIME:\tRun Total 0.0232 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0423 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:41:55,930 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704&amp;#x27;, &amp;#x27;1640baa8-32bc-462c-86b7-721997822f47&amp;#x27;]\n2025-01-08 09:41:55,930 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/cpptraj_strip/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/cpptraj_strip/output.netcdf\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.strip.netcdf\n     SIZE_A: 6298620 bytes\n     SIZE_B: 6298620 bytes\n     TOLERANCE: 1.0%, Low: 6235633.8 bytes, High: 6361606.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_strip Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:82 /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704 directory successfully created\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:63 cpptraj -i 1640baa8-32bc-462c-86b7-721997822f47/instructions.in\n\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 1640baa8-32bc-462c-86b7-721997822f47/instructions.in...\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:41:55\n| Available memory: 10.506 GB\n\nINPUT: Reading input from &amp;#x27;1640baa8-32bc-462c-86b7-721997822f47/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip @CA]\n    STRIP: Stripping atoms in mask [@CA]\n  [trajout /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip @CA]\n\tStripping 710 atoms.\n\tStripped topology: 10497 atoms, 710 res, box: None, 2100 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2190.1007 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.03%)\nTIME:\t\tTrajectory Process : 0.0228 s ( 98.46%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0003 s (  0.02%)\nTIME:\tRun Total 0.0232 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0423 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/cpptraj_strip/sandbox_3d68e2f6-35c9-4bf4-a993-e5de58411704&amp;#x27;, &amp;#x27;1640baa8-32bc-462c-86b7-721997822f47&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_cluster.py::TestGMXCluster::test_cluster&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_cluster.py::TestGMXCluster::test_cluster&#34;, &#34;duration&#34;: &#34;00:00:18&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_cluster.py::TestGMXCluster::test_cluster&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:18&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:41:56,165 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_cluster Version: 5.0.1\n2025-01-08 09:41:56,166 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265 directory successfully created\n2025-01-08 09:41:56,167 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\n2025-01-08 09:41:56,171 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\n2025-01-08 09:41:56,172 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\n2025-01-08 09:41:56,172 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_cluster/281be8f0-1445-4625-87a5-7e49cb31ac89.stdin to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\n2025-01-08 09:41:56,172 [MainThread  ] [INFO ]  gmx cluster -g /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr -f /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/trajectory.trr -cl /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/281be8f0-1445-4625-87a5-7e49cb31ac89.stdin\n\n2025-01-08 09:41:56,872 [MainThread  ] [INFO ]  Executing: gmx cluster -g /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d...\n2025-01-08 09:41:56,873 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:41:56,873 [MainThread  ] [INFO ]  Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:41:56,873 [MainThread  ] [INFO ]                 :-) GROMACS - gmx cluster, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_cluster\nCommand line:\n  gmx cluster -g /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr -f /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/trajectory.trr -cl /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/index.ndx\n\nUsing linkage method for clustering\nReading file /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr, VERSION 2019.1 (single precision)\n\nSelect group for least squares fit and RMSD calculation:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: \nSelect group for output:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAllocated 7082160 bytes for frames\nRead 11 frames from trajectory /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/trajectory.trr\nComputing 11x11 RMS deviation matrix\n\r# RMSD calculations left: 45   \r# RMSD calculations left: 36   \r# RMSD calculations left: 28   \r# RMSD calculations left: 21   \r# RMSD calculations left: 15   \r# RMSD calculations left: 10   \r# RMSD calculations left: 6   \r# RMSD calculations left: 3   \r# RMSD calculations left: 1   \r# RMSD calculations left: 0   \r# RMSD calculations left: 0   \n\nThe RMSD ranges from 1.80823 to 3.12553 nm\nAverage RMSD is 2.45651\nNumber of structures for matrix 11\nEnergy of the matrix is 34.476.\nWARNING: rmsd cutoff 0.1 is outside range of rmsd values 1.80823 to 3.12553\nWARNING: rmsd minimum 0 is below lowest rmsd value 1.80823\nLinking structures *\nSorting and renumbering clusters\n\nFound 11 clusters\n\nWriting middle structure for each cluster to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/output_pdb.pdb\nWriting rms distance/clustering matrix   9%\b\b\b\b 18%\b\b\b\b 27%\b\b\b\b 36%\b\b\b\b 45%\b\b\b\b 54%\b\b\b\b 63%\b\b\b\b 72%\b\b\b\b 81%\b\b\b\b 90%\b\b\b\b100%\b\b\b\b\n\nGROMACS reminds you: &amp;quot;No matter how important you are, you are not as important as lunch.&amp;quot; (Randy Pausch)\n\n\n2025-01-08 09:41:56,892 [MainThread  ] [INFO ]  Removed: [&amp;#x27;gmx_cluster_rmsd-dist.xvg&amp;#x27;, &amp;#x27;gmx_cluster_rmsd-clust.xpm&amp;#x27;, &amp;#x27;gmx_cluster_cluster.log&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_cluster/281be8f0-1445-4625-87a5-7e49cb31ac89.stdin&amp;#x27;]\n2025-01-08 09:41:56,893 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_cluster/output_pdb.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_6/gmx_cluster/output_pdb.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_cluster.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 4.104104623905199e-05\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_cluster Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_cluster/281be8f0-1445-4625-87a5-7e49cb31ac89.stdin to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:63 gmx cluster -g /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr -f /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/trajectory.trr -cl /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/281be8f0-1445-4625-87a5-7e49cb31ac89.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:36 Executing: gmx cluster -g /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d...\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:41 Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx cluster, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_cluster\nCommand line:\n  gmx cluster -g /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr -f /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/trajectory.trr -cl /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/index.ndx\n\nUsing linkage method for clustering\nReading file /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/topology.tpr, VERSION 2019.1 (single precision)\n\nSelect group for least squares fit and RMSD calculation:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: \nSelect group for output:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAllocated 7082160 bytes for frames\nRead 11 frames from trajectory /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/trajectory.trr\nComputing 11x11 RMS deviation matrix\n\r# RMSD calculations left: 45   \r# RMSD calculations left: 36   \r# RMSD calculations left: 28   \r# RMSD calculations left: 21   \r# RMSD calculations left: 15   \r# RMSD calculations left: 10   \r# RMSD calculations left: 6   \r# RMSD calculations left: 3   \r# RMSD calculations left: 1   \r# RMSD calculations left: 0   \r# RMSD calculations left: 0   \n\nThe RMSD ranges from 1.80823 to 3.12553 nm\nAverage RMSD is 2.45651\nNumber of structures for matrix 11\nEnergy of the matrix is 34.476.\nWARNING: rmsd cutoff 0.1 is outside range of rmsd values 1.80823 to 3.12553\nWARNING: rmsd minimum 0 is below lowest rmsd value 1.80823\nLinking structures *\nSorting and renumbering clusters\n\nFound 11 clusters\n\nWriting middle structure for each cluster to /tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265/output_pdb.pdb\nWriting rms distance/clustering matrix   9%\b\b\b\b 18%\b\b\b\b 27%\b\b\b\b 36%\b\b\b\b 45%\b\b\b\b 54%\b\b\b\b 63%\b\b\b\b 72%\b\b\b\b 81%\b\b\b\b 90%\b\b\b\b100%\b\b\b\b\n\nGROMACS reminds you: &amp;quot;No matter how important you are, you are not as important as lunch.&amp;quot; (Randy Pausch)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Removed: [&amp;#x27;gmx_cluster_rmsd-dist.xvg&amp;#x27;, &amp;#x27;gmx_cluster_rmsd-clust.xpm&amp;#x27;, &amp;#x27;gmx_cluster_cluster.log&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_cluster/sandbox_040211f4-2c97-4f7a-a90d-ae0f327f1265&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_cluster/281be8f0-1445-4625-87a5-7e49cb31ac89.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_cluster/gmx_cluster_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_energy.py::TestGMXEnergy::test_energy&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_energy.py::TestGMXEnergy::test_energy&#34;, &#34;duration&#34;: &#34;221 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_energy.py::TestGMXEnergy::test_energy&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;221 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:14,163 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_energy Version: 5.0.1\n2025-01-08 09:42:14,164 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1 directory successfully created\n2025-01-08 09:42:14,164 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/energy.edr to /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1\n2025-01-08 09:42:14,164 [MainThread  ] [INFO ]  gmx energy -f /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/energy.edr -o /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/output.xvg -xvg none &amp;lt; b4491515-967d-4fd3-ac7c-c95fc5d0a301/instructions.in\n\n2025-01-08 09:42:14,175 [MainThread  ] [INFO ]  Executing: gmx energy -f /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b...\n2025-01-08 09:42:14,175 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:14,175 [MainThread  ] [INFO ]  \nStatistics over 501 steps [ 0.0000 through 1.0000 ps ], 2 data sets\nAll statistics are over 51 points\n\nEnergy                      Average   Err.Est.       RMSD  Tot-Drift\n-------------------------------------------------------------------------------\nPotential                -2.39705e+06         --    1223.89    6280.48  (kJ/mol)\nPressure                   0.342962         --    73.8495    27.2604  (bar)\n\n2025-01-08 09:42:14,175 [MainThread  ] [INFO ]                  :-) GROMACS - gmx energy, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_energy\nCommand line:\n  gmx energy -f /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/energy.edr -o /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/output.xvg -xvg none\n\nOpened /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/energy.edr as single precision energy file\n\nSelect the terms you want from the following list by\nselecting either (part of) the name or the number or a combination.\nEnd your selection with an empty line or a zero.\n-------------------------------------------------------------------\n  1  Angle            2  Proper-Dih.      3  Improper-Dih.    4  LJ-14         \n  5  Coulomb-14       6  LJ-(SR)          7  Coulomb-(SR)     8  Coul.-recip.  \n  9  Position-Rest.  10  Potential       11  Kinetic-En.     12  Total-Energy  \n 13  Temperature     14  Pressure        15  Constr.-rmsd    16  Box-X         \n 17  Box-Y           18  Box-Z           19  Volume          20  Density       \n 21  pV              22  Enthalpy        23  Vir-XX          24  Vir-XY        \n 25  Vir-XZ          26  Vir-YX          27  Vir-YY          28  Vir-YZ        \n 29  Vir-ZX          30  Vir-ZY          31  Vir-ZZ          32  Pres-XX       \n 33  Pres-XY         34  Pres-XZ         35  Pres-YX         36  Pres-YY       \n 37  Pres-YZ         38  Pres-ZX         39  Pres-ZY         40  Pres-ZZ       \n 41  #Surf*SurfTen   42  Box-Vel-XX      43  Box-Vel-YY      44  Box-Vel-ZZ    \n 45  Mu-X            46  Mu-Y            47  Mu-Z            48  T-Protein     \n 49  T-non-Protein                       50  Lamb-Protein                      \n 51  Lamb-non-Protein                  \n\n\rReading energy frame      0 time    0.000         \rReading energy frame      1 time    1.000         \rLast energy frame read 1 time    1.000         \n\nGROMACS reminds you: &amp;quot;I don&amp;#x27;t know how many of you have ever met Dijkstra, but you probably know that arrogance in computer science is measured in nano-Dijkstras.&amp;quot; (Alan Kay)\n\n\n2025-01-08 09:42:14,176 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1&amp;#x27;, &amp;#x27;b4491515-967d-4fd3-ac7c-c95fc5d0a301&amp;#x27;]\n2025-01-08 09:42:14,176 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_energy/output.xvg\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/gmx_energy/output.xvg\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_energy.xvg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_energy Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/energy.edr to /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:63 gmx energy -f /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/energy.edr -o /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/output.xvg -xvg none &amp;lt; b4491515-967d-4fd3-ac7c-c95fc5d0a301/instructions.in\n\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:36 Executing: gmx energy -f /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b...\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:41 \nStatistics over 501 steps [ 0.0000 through 1.0000 ps ], 2 data sets\nAll statistics are over 51 points\n\nEnergy                      Average   Err.Est.       RMSD  Tot-Drift\n-------------------------------------------------------------------------------\nPotential                -2.39705e+06         --    1223.89    6280.48  (kJ/mol)\nPressure                   0.342962         --    73.8495    27.2604  (bar)\n\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.err:cmd_wrapper.py:49                 :-) GROMACS - gmx energy, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_energy\nCommand line:\n  gmx energy -f /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/energy.edr -o /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/output.xvg -xvg none\n\nOpened /tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1/energy.edr as single precision energy file\n\nSelect the terms you want from the following list by\nselecting either (part of) the name or the number or a combination.\nEnd your selection with an empty line or a zero.\n-------------------------------------------------------------------\n  1  Angle            2  Proper-Dih.      3  Improper-Dih.    4  LJ-14         \n  5  Coulomb-14       6  LJ-(SR)          7  Coulomb-(SR)     8  Coul.-recip.  \n  9  Position-Rest.  10  Potential       11  Kinetic-En.     12  Total-Energy  \n 13  Temperature     14  Pressure        15  Constr.-rmsd    16  Box-X         \n 17  Box-Y           18  Box-Z           19  Volume          20  Density       \n 21  pV              22  Enthalpy        23  Vir-XX          24  Vir-XY        \n 25  Vir-XZ          26  Vir-YX          27  Vir-YY          28  Vir-YZ        \n 29  Vir-ZX          30  Vir-ZY          31  Vir-ZZ          32  Pres-XX       \n 33  Pres-XY         34  Pres-XZ         35  Pres-YX         36  Pres-YY       \n 37  Pres-YZ         38  Pres-ZX         39  Pres-ZY         40  Pres-ZZ       \n 41  #Surf*SurfTen   42  Box-Vel-XX      43  Box-Vel-YY      44  Box-Vel-ZZ    \n 45  Mu-X            46  Mu-Y            47  Mu-Z            48  T-Protein     \n 49  T-non-Protein                       50  Lamb-Protein                      \n 51  Lamb-non-Protein                  \n\n\rReading energy frame      0 time    0.000         \rReading energy frame      1 time    1.000         \rLast energy frame read 1 time    1.000         \n\nGROMACS reminds you: &amp;quot;I don&amp;#x27;t know how many of you have ever met Dijkstra, but you probably know that arrogance in computer science is measured in nano-Dijkstras.&amp;quot; (Alan Kay)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_energy/sandbox_94346ce1-9341-44bf-b643-b50219f671d1&amp;#x27;, &amp;#x27;b4491515-967d-4fd3-ac7c-c95fc5d0a301&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_energy/gmx_energy_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_image.py::TestGMXImage::test_image&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_image.py::TestGMXImage::test_image&#34;, &#34;duration&#34;: &#34;326 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_image.py::TestGMXImage::test_image&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;326 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:14,398 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_image Version: 5.0.1\n2025-01-08 09:42:14,398 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9 directory successfully created\n2025-01-08 09:42:14,403 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\n2025-01-08 09:42:14,405 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\n2025-01-08 09:42:14,405 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\n2025-01-08 09:42:14,405 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_image/01f98031-8ee2-4459-ac62-c2c8ecaa9107.stdin to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\n2025-01-08 09:42:14,405 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/trajectory.trr -s /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/output.xtc -n /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/index.ndx -center &amp;lt; /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/01f98031-8ee2-4459-ac62-c2c8ecaa9107.stdin\n\n2025-01-08 09:42:14,502 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-6...\n2025-01-08 09:42:14,502 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:14,502 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for least squares fit\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for centering\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:42:14,502 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_image\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/trajectory.trr -s /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/output.xtc -n /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/index.ndx -center\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nReading file /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;I don&amp;#x27;t know how many of you have ever met Dijkstra, but you probably know that arrogance in computer science is measured in nano-Dijkstras.&amp;quot; (Alan Kay)\n\n\n2025-01-08 09:42:14,504 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_image/01f98031-8ee2-4459-ac62-c2c8ecaa9107.stdin&amp;#x27;]\n2025-01-08 09:42:14,505 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_image/output.xtc\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/gmx_image/output.xtc\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_image.xtc\n     SIZE_A: 1167844 bytes\n     SIZE_B: 1167844 bytes\n     TOLERANCE: 1.0%, Low: 1156165.56 bytes, High: 1179522.44 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_image Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_image/01f98031-8ee2-4459-ac62-c2c8ecaa9107.stdin to /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/trajectory.trr -s /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/output.xtc -n /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/index.ndx -center &amp;lt; /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/01f98031-8ee2-4459-ac62-c2c8ecaa9107.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-6...\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for least squares fit\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for centering\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_image\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/trajectory.trr -s /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/output.xtc -n /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/index.ndx -center\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nReading file /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;I don&amp;#x27;t know how many of you have ever met Dijkstra, but you probably know that arrogance in computer science is measured in nano-Dijkstras.&amp;quot; (Alan Kay)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_image/sandbox_8a3a731e-777b-4cfe-9ab9-67a26ccab4f9&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_image/01f98031-8ee2-4459-ac62-c2c8ecaa9107.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_image/gmx_image_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rgyr.py::TestGMXRgyr::test_rgyr&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rgyr.py::TestGMXRgyr::test_rgyr&#34;, &#34;duration&#34;: &#34;294 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_rgyr.py::TestGMXRgyr::test_rgyr&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;294 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:14,715 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_rgyr Version: 5.0.1\n2025-01-08 09:42:14,715 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c directory successfully created\n2025-01-08 09:42:14,716 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\n2025-01-08 09:42:14,721 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\n2025-01-08 09:42:14,721 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\n2025-01-08 09:42:14,721 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_rgyr/7b48d6f4-5022-4dba-be0f-b05e0bd1ea4f.stdin to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\n2025-01-08 09:42:14,722 [MainThread  ] [INFO ]  gmx gyrate -s /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr -f /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/7b48d6f4-5022-4dba-be0f-b05e0bd1ea4f.stdin\n\n2025-01-08 09:42:14,797 [MainThread  ] [INFO ]  Executing: gmx gyrate -s /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca...\n2025-01-08 09:42:14,797 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:14,797 [MainThread  ] [INFO ]                  :-) GROMACS - gmx gyrate, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_rgyr\nCommand line:\n  gmx gyrate -s /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr -f /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/index.ndx\n\nReading file /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr, VERSION 2019.1 (single precision)\ntrr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAnalyzed 11 frames, last time 100.000\n\nGROMACS reminds you: &amp;quot;I don&amp;#x27;t know how many of you have ever met Dijkstra, but you probably know that arrogance in computer science is measured in nano-Dijkstras.&amp;quot; (Alan Kay)\n\n\n2025-01-08 09:42:14,799 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_rgyr/7b48d6f4-5022-4dba-be0f-b05e0bd1ea4f.stdin&amp;#x27;]\n2025-01-08 09:42:14,799 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_rgyr/output.xvg\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/gmx_rgyr/output.xvg\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_rgyr.xvg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_rgyr Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_rgyr/7b48d6f4-5022-4dba-be0f-b05e0bd1ea4f.stdin to /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:cmd_wrapper.py:63 gmx gyrate -s /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr -f /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/7b48d6f4-5022-4dba-be0f-b05e0bd1ea4f.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:cmd_wrapper.py:36 Executing: gmx gyrate -s /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca...\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.err:cmd_wrapper.py:49                 :-) GROMACS - gmx gyrate, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_rgyr\nCommand line:\n  gmx gyrate -s /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr -f /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/index.ndx\n\nReading file /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c/topology.tpr, VERSION 2019.1 (single precision)\ntrr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAnalyzed 11 frames, last time 100.000\n\nGROMACS reminds you: &amp;quot;I don&amp;#x27;t know how many of you have ever met Dijkstra, but you probably know that arrogance in computer science is measured in nano-Dijkstras.&amp;quot; (Alan Kay)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_rgyr/sandbox_84b8b419-ee6d-4299-81f8-7ca473ba1e8c&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_rgyr/7b48d6f4-5022-4dba-be0f-b05e0bd1ea4f.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rms.py::TestGMXRms::test_rms&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rms.py::TestGMXRms::test_rms&#34;, &#34;duration&#34;: &#34;296 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_rms.py::TestGMXRms::test_rms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;296 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:15,010 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_rms Version: 5.0.1\n2025-01-08 09:42:15,011 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95 directory successfully created\n2025-01-08 09:42:15,012 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\n2025-01-08 09:42:15,017 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\n2025-01-08 09:42:15,017 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\n2025-01-08 09:42:15,017 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_rms/0d304ae8-1f5b-4b5b-9745-494e08f960d1.stdin to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\n2025-01-08 09:42:15,018 [MainThread  ] [INFO ]  gmx rms -s /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr -f /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/0d304ae8-1f5b-4b5b-9745-494e08f960d1.stdin\n\n2025-01-08 09:42:15,096 [MainThread  ] [INFO ]  Executing: gmx rms -s /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f621...\n2025-01-08 09:42:15,096 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:15,096 [MainThread  ] [INFO ]  Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:42:15,096 [MainThread  ] [INFO ]                   :-) GROMACS - gmx rms, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_rms\nCommand line:\n  gmx rms -s /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr -f /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/index.ndx\n\nReading file /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr, VERSION 2019.1 (single precision)\nSelect group for least squares fit\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Select group for RMSD calculation\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \n\nGROMACS reminds you: &amp;quot;We must be clear that when it comes to atoms, language can be used only as in poetry. &amp;quot; (Niels Bohr)\n\n\n2025-01-08 09:42:15,098 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_rms/0d304ae8-1f5b-4b5b-9745-494e08f960d1.stdin&amp;#x27;]\n2025-01-08 09:42:15,098 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_rms/output.xvg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_rms/0d304ae8-1f5b-4b5b-9745-494e08f960d1.stdin to /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:63 gmx rms -s /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr -f /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/0d304ae8-1f5b-4b5b-9745-494e08f960d1.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:36 Executing: gmx rms -s /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f621...\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:41 Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.err:cmd_wrapper.py:49                  :-) GROMACS - gmx rms, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_rms\nCommand line:\n  gmx rms -s /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr -f /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/trajectory.trr -o /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/output.xvg -xvg none -n /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/index.ndx\n\nReading file /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95/topology.tpr, VERSION 2019.1 (single precision)\nSelect group for least squares fit\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Select group for RMSD calculation\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \n\nGROMACS reminds you: &amp;quot;We must be clear that when it comes to atoms, language can be used only as in poetry. &amp;quot; (Niels Bohr)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_rms/sandbox_a9ab2c73-6430-4f11-8fac-696f62100d95&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_rms/0d304ae8-1f5b-4b5b-9745-494e08f960d1.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_rms/gmx_rms_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str.py::TestGMXTrjConvStr::test_trjconv_str&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str.py::TestGMXTrjConvStr::test_trjconv_str&#34;, &#34;duration&#34;: &#34;00:00:17&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str.py::TestGMXTrjConvStr::test_trjconv_str&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:17&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:15,307 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_trjconv_str Version: 5.0.1\n2025-01-08 09:42:15,307 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50 directory successfully created\n2025-01-08 09:42:15,312 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\n2025-01-08 09:42:15,313 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\n2025-01-08 09:42:15,314 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\n2025-01-08 09:42:15,314 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_trjconv_str/4c2930d6-0333-4b53-a441-9d4715da88bc.stdin to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\n2025-01-08 09:42:15,314 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr -o /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/output.pdb -nocenter -n /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/4c2930d6-0333-4b53-a441-9d4715da88bc.stdin\n\n2025-01-08 09:42:15,919 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-...\n2025-01-08 09:42:15,919 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:15,919 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:42:15,919 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_trjconv_str\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr -o /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/output.pdb -nocenter -n /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;We must be clear that when it comes to atoms, language can be used only as in poetry. &amp;quot; (Niels Bohr)\n\n\n2025-01-08 09:42:15,940 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str/4c2930d6-0333-4b53-a441-9d4715da88bc.stdin&amp;#x27;]\n2025-01-08 09:42:15,940 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_trjconv_str/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_6/gmx_trjconv_str/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_trjconv.str.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 4.967442854363623e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_trjconv_str Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_trjconv_str/4c2930d6-0333-4b53-a441-9d4715da88bc.stdin to /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr -o /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/output.pdb -nocenter -n /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/4c2930d6-0333-4b53-a441-9d4715da88bc.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-...\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_trjconv_str\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr -o /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/output.pdb -nocenter -n /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;We must be clear that when it comes to atoms, language can be used only as in poetry. &amp;quot; (Niels Bohr)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str/sandbox_2d3799bd-4851-44b6-bc5f-fb267e370e50&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str/4c2930d6-0333-4b53-a441-9d4715da88bc.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str_ens.py::TestGMXTrjConvStrEns::test_trjconv_str_ens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str_ens.py::TestGMXTrjConvStrEns::test_trjconv_str_ens&#34;, &#34;duration&#34;: &#34;00:00:04&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str_ens.py::TestGMXTrjConvStrEns::test_trjconv_str_ens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:32,732 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_trjconv_str_ens Version: 5.0.1\n2025-01-08 09:42:32,733 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808 directory successfully created\n2025-01-08 09:42:32,738 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\n2025-01-08 09:42:32,739 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\n2025-01-08 09:42:32,739 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\n2025-01-08 09:42:32,739 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_trjconv_str_ens/33ad1b19-4eba-4345-a48f-4b8a074bc5a2.stdin to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\n2025-01-08 09:42:32,740 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output.pdb -e 10 -n /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/33ad1b19-4eba-4345-a48f-4b8a074bc5a2.stdin\n\n2025-01-08 09:42:32,870 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-4...\n2025-01-08 09:42:32,870 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:32,870 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:42:32,870 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_trjconv_str_ens\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output.pdb -e 10 -n /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rLast frame          1 time   10.000   \n -&amp;gt;  frame      1 time   10.000      \r\nLast written: frame      1 time   10.000\n\n\nGROMACS reminds you: &amp;quot;I&amp;#x27;m a strong believer that ignorance is important in science. If you know too much, you start seeing reasons why things won&amp;#x27;t work. That&amp;#x27;s why its important to change your field to collect more ignorance.&amp;quot; (Sydney Brenner)\n\n\n2025-01-08 09:42:32,881 [MainThread  ] [INFO ]  Adding:\n2025-01-08 09:42:32,881 [MainThread  ] [INFO ]  [PosixPath(&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output0.pdb&amp;#x27;), PosixPath(&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output1.pdb&amp;#x27;)]\n2025-01-08 09:42:32,881 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output.zip\n2025-01-08 09:42:32,886 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/33ad1b19-4eba-4345-a48f-4b8a074bc5a2.stdin&amp;#x27;]\n2025-01-08 09:42:32,887 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_trjconv_str_ens/output.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_6/gmx_trjconv_str_ens/output.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_trjconv.str.ens.zip\nChecking RMSD between:\n     PDB_A: 6659efe3-57ce-4b1d-9913-ab2de981386e/output0.pdb\n     PDB_B: a0c6e34c-b109-4ff1-ab16-056c85fbe232/output0.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 4.967442854363623e-15\n     RMS_CUTOFF: 1\nChecking RMSD between:\n     PDB_A: 6659efe3-57ce-4b1d-9913-ab2de981386e/output1.pdb\n     PDB_B: a0c6e34c-b109-4ff1-ab16-056c85fbe232/output1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 9.298654174020101e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_trjconv_str_ens Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_trjconv_str_ens/33ad1b19-4eba-4345-a48f-4b8a074bc5a2.stdin to /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output.pdb -e 10 -n /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/33ad1b19-4eba-4345-a48f-4b8a074bc5a2.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-4...\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_trjconv_str_ens\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/trajectory.trr -s /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output.pdb -e 10 -n /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rLast frame          1 time   10.000   \n -&amp;gt;  frame      1 time   10.000      \r\nLast written: frame      1 time   10.000\n\n\nGROMACS reminds you: &amp;quot;I&amp;#x27;m a strong believer that ignorance is important in science. If you know too much, you start seeing reasons why things won&amp;#x27;t work. That&amp;#x27;s why its important to change your field to collect more ignorance.&amp;quot; (Sydney Brenner)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:149 [PosixPath(&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output0.pdb&amp;#x27;), PosixPath(&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output1.pdb&amp;#x27;)]\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:150 to: /tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808/output.zip\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/sandbox_7af5c3f4-1f30-461d-a82f-dc0148cb5808&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_str_ens/33ad1b19-4eba-4345-a48f-4b8a074bc5a2.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_trj.py::TestGMXTrjConvTrj::test_trjconv_trj&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_trj.py::TestGMXTrjConvTrj::test_trjconv_trj&#34;, &#34;duration&#34;: &#34;238 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_trj.py::TestGMXTrjConvTrj::test_trjconv_trj&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;238 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:42:37,017 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_trjconv_trj Version: 5.0.1\n2025-01-08 09:42:37,017 [MainThread  ] [INFO ]  /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694 directory successfully created\n2025-01-08 09:42:37,022 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694\n2025-01-08 09:42:37,023 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694\n2025-01-08 09:42:37,023 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_6/gmx_trjconv_trj/469418a3-296d-4691-9696-22df94881339.stdin to /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694\n2025-01-08 09:42:37,023 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/output.xtc -n /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/469418a3-296d-4691-9696-22df94881339.stdin\n\n2025-01-08 09:42:37,045 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-...\n2025-01-08 09:42:37,045 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:42:37,045 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:42:37,045 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_trjconv_trj\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/output.xtc -n /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/index.ndx\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rLast frame          0 time    0.000   \n -&amp;gt;  frame      0 time    0.000      \r\nLast written: frame      0 time    0.000\n\n\nGROMACS reminds you: &amp;quot;Never mind, death professor, your structure&amp;#x27;s fine&amp;quot; (TV on the Radio)\n\n\n2025-01-08 09:42:37,047 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_trj/469418a3-296d-4691-9696-22df94881339.stdin&amp;#x27;]\n2025-01-08 09:42:37,047 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_6/gmx_trjconv_trj/output.xtc\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_6/gmx_trjconv_trj/output.xtc\n     FILE_B: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_trjconv.trj.xtc\n     SIZE_A: 108280 bytes\n     SIZE_B: 108280 bytes\n     TOLERANCE: 1.0%, Low: 107197.2 bytes, High: 109362.8 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_trjconv_trj Version: 5.0.1\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:82 /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694 directory successfully created\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_6/gmx_trjconv_trj/469418a3-296d-4691-9696-22df94881339.stdin to /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/output.xtc -n /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/index.ndx &amp;lt; /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/469418a3-296d-4691-9696-22df94881339.stdin\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-...\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_6/gmx_trjconv_trj\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/output.xtc -n /tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694/index.ndx\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rLast frame          0 time    0.000   \n -&amp;gt;  frame      0 time    0.000      \r\nLast written: frame      0 time    0.000\n\n\nGROMACS reminds you: &amp;quot;Never mind, death professor, your structure&amp;#x27;s fine&amp;quot; (TV on the Radio)\n\n\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_trj/sandbox_c87eeab6-e312-4476-af94-74e323651694&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_6/gmx_trjconv_trj/469418a3-296d-4691-9696-22df94881339.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_6/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_6\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.21&#34;, &#34;Platform&#34;: &#34;Linux-5.15.0-125-generic-x86_64-with-glibc2.35&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.4&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;html&#34;: &#34;4.1.1&#34;, &#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_average.py::TestCpptrajAverage::test_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_average.py::TestCpptrajAverage::test_average&#34;, &#34;duration&#34;: &#34;746 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_average.py::TestCpptrajAverage::test_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;746 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:18,080 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_average Version: 5.0.1\n2025-01-08 09:44:18,081 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5 directory successfully created\n2025-01-08 09:44:18,094 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5\n2025-01-08 09:44:18,116 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5\n2025-01-08 09:44:18,117 [MainThread  ] [INFO ]  cpptraj -i c5e53a77-2ec2-46af-883b-777e5d20362c/instructions.in\n\n2025-01-08 09:44:18,211 [MainThread  ] [INFO ]  Executing: cpptraj -i c5e53a77-2ec2-46af-883b-777e5d20362c/instructions.in...\n2025-01-08 09:44:18,212 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:18,212 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:18\n| Available memory: 2.914 GB\n\nINPUT: Reading input from &amp;#x27;c5e53a77-2ec2-46af-883b-777e5d20362c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb&amp;#x27; as PDB\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tWriting averaged coords to file &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb pdb]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2914.2624 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames,  &amp;#x27;output.pdb&amp;#x27; is a PDB file, Parm cpptraj.parm.top: Writing 1 frames (1-Last, 1)\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0172 s ( 80.72%)\nTIME:\t\tAction Post        : 0.0040 s ( 18.73%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.09%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0213 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0555 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:18,216 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5&amp;#x27;, &amp;#x27;c5e53a77-2ec2-46af-883b-777e5d20362c&amp;#x27;]\n2025-01-08 09:44:18,217 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_average/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_2/cpptraj_average/output.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.average.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 710\n     Atoms ALIGNED in PDB_B: 710\n     RMS: 1.3031036158232704e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_average Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:63 cpptraj -i c5e53a77-2ec2-46af-883b-777e5d20362c/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i c5e53a77-2ec2-46af-883b-777e5d20362c/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:18\n| Available memory: 2.914 GB\n\nINPUT: Reading input from &amp;#x27;c5e53a77-2ec2-46af-883b-777e5d20362c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb&amp;#x27; as PDB\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tWriting averaged coords to file &amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average /tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5/output.pdb pdb]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2914.2624 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames,  &amp;#x27;output.pdb&amp;#x27; is a PDB file, Parm cpptraj.parm.top: Writing 1 frames (1-Last, 1)\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0172 s ( 80.72%)\nTIME:\t\tAction Post        : 0.0040 s ( 18.73%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.09%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0213 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0555 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_average/sandbox_89d08d3c-1fea-452a-9f1c-e004a5c7fbb5&amp;#x27;, &amp;#x27;c5e53a77-2ec2-46af-883b-777e5d20362c&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_average/cpptraj_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorFirst::test_bfactor_first&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorFirst::test_bfactor_first&#34;, &#34;duration&#34;: &#34;591 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorFirst::test_bfactor_first&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;591 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:18,881 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\n2025-01-08 09:44:18,882 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012 directory successfully created\n2025-01-08 09:44:18,889 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012\n2025-01-08 09:44:18,901 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012\n2025-01-08 09:44:18,902 [MainThread  ] [INFO ]  cpptraj -i e46185c9-0e07-4aa4-8884-af88983c61bd/instructions.in\n\n2025-01-08 09:44:18,994 [MainThread  ] [INFO ]  Executing: cpptraj -i e46185c9-0e07-4aa4-8884-af88983c61bd/instructions.in...\n2025-01-08 09:44:18,994 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:18,995 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:18\n| Available memory: 2.913 GB\n\nINPUT: Reading input from &amp;#x27;e46185c9-0e07-4aa4-8884-af88983c61bd/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2799.7088 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0179 s ( 92.17%)\nTIME:\t\tAction Post        : 0.0001 s (  0.70%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0013 s (  6.79%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0194 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0536 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:18,999 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012&amp;#x27;, &amp;#x27;e46185c9-0e07-4aa4-8884-af88983c61bd&amp;#x27;]\n2025-01-08 09:44:19,000 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_bfactor_first/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_bfactor_first/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.first.dat\n        File_A hash: b&amp;quot;\\x83\\x86\\xed &amp;#x27;\\x03v\\x965\\x10\\xae!)\\x1f\\x8d\\xbat(  \\x92\\xb3w\\x08 \\xafjz\\n\\xf0\\x9b\\x02&amp;quot;\n        File_B hash: b&amp;quot;\\x83\\x86\\xed &amp;#x27;\\x03v\\x965\\x10\\xae!)\\x1f\\x8d\\xbat(  \\x92\\xb3w\\x08 \\xafjz\\n\\xf0\\x9b\\x02&amp;quot;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:63 cpptraj -i e46185c9-0e07-4aa4-8884-af88983c61bd/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:36 Executing: cpptraj -i e46185c9-0e07-4aa4-8884-af88983c61bd/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:18\n| Available memory: 2.913 GB\n\nINPUT: Reading input from &amp;#x27;e46185c9-0e07-4aa4-8884-af88983c61bd/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2799.7088 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0179 s ( 92.17%)\nTIME:\t\tAction Post        : 0.0001 s (  0.70%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0013 s (  6.79%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0194 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0536 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_first/sandbox_6a2ee780-5aee-4bf6-82e4-b8b57351d012&amp;#x27;, &amp;#x27;e46185c9-0e07-4aa4-8884-af88983c61bd&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_first/cpptraj_bfactor_first_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorAverage::test_bfactor_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorAverage::test_bfactor_average&#34;, &#34;duration&#34;: &#34;589 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorAverage::test_bfactor_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;589 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:19,458 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\n2025-01-08 09:44:19,459 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d directory successfully created\n2025-01-08 09:44:19,466 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d\n2025-01-08 09:44:19,477 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d\n2025-01-08 09:44:19,478 [MainThread  ] [INFO ]  cpptraj -i f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35/instructions.in\n\n2025-01-08 09:44:19,586 [MainThread  ] [INFO ]  Executing: cpptraj -i f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35/instructions.in...\n2025-01-08 09:44:19,587 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:19,588 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:19\n| Available memory: 2.912 GB\n\nINPUT: Reading input from &amp;#x27;f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2570.2976 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0195 s ( 97.88%)\nTIME:\t\tAction Post        : 0.0003 s (  1.41%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.24%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0199 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/output.dat byres bfactor]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 4361.8599 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0115 s ( 77.78%)\nTIME:\t\tAction Post        : 0.0012 s (  8.37%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0020 s ( 13.66%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0147 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0724 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:19,592 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d&amp;#x27;, &amp;#x27;f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35&amp;#x27;]\n2025-01-08 09:44:19,593 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_bfactor_average/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_bfactor_average/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.average.dat\n        File_A hash: b&amp;#x27;\\x8d\\x1e\\xa1\\xbaL\\x95\\xf2\\x86\\x0eI\\xd0\\x06\\xff\\xb1\\xfe;\\xe8&amp;amp;^\\xf6\\x8f\\x00\\x18\\xab\\x1dy\\xacC:\\tR\\x16&amp;#x27;\n        File_B hash: b&amp;#x27;\\x8d\\x1e\\xa1\\xbaL\\x95\\xf2\\x86\\x0eI\\xd0\\x06\\xff\\xb1\\xfe;\\xe8&amp;amp;^\\xf6\\x8f\\x00\\x18\\xab\\x1dy\\xacC:\\tR\\x16&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:63 cpptraj -i f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:19\n| Available memory: 2.912 GB\n\nINPUT: Reading input from &amp;#x27;f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2570.2976 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0195 s ( 97.88%)\nTIME:\t\tAction Post        : 0.0003 s (  1.41%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.24%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0199 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d/output.dat byres bfactor]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 4361.8599 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0115 s ( 77.78%)\nTIME:\t\tAction Post        : 0.0012 s (  8.37%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0020 s ( 13.66%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0147 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0724 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_average/sandbox_43204fe1-c241-4856-9355-1044d71fb86d&amp;#x27;, &amp;#x27;f7d7cc6d-b10b-4dc8-a8cc-6e1e7c625b35&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_average/cpptraj_bfactor_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorExperimental::test_bfactor_experimental&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorExperimental::test_bfactor_experimental&#34;, &#34;duration&#34;: &#34;632 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_bfactor.py::TestCpptrajBfactorExperimental::test_bfactor_experimental&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;632 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:20,071 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\n2025-01-08 09:44:20,072 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c directory successfully created\n2025-01-08 09:44:20,079 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c\n2025-01-08 09:44:20,091 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c\n2025-01-08 09:44:20,094 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c\n2025-01-08 09:44:20,095 [MainThread  ] [INFO ]  cpptraj -i 2ba481c2-1395-4057-9432-cd96bff4fcfe/instructions.in\n\n2025-01-08 09:44:20,223 [MainThread  ] [INFO ]  Executing: cpptraj -i 2ba481c2-1395-4057-9432-cd96bff4fcfe/instructions.in...\n2025-01-08 09:44:20,224 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:20,224 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:20\n| Available memory: 2.908 GB\n\nINPUT: Reading input from &amp;#x27;2ba481c2-1395-4057-9432-cd96bff4fcfe/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2281.5423 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.17%)\nTIME:\t\tTrajectory Process : 0.0219 s ( 92.88%)\nTIME:\t\tAction Post        : 0.0001 s (  0.36%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0013 s (  5.69%)\nTIME:\t\tOther              : 0.0002 s (  0.01%)\nTIME:\tRun Total 0.0236 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0867 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:20,229 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c&amp;#x27;, &amp;#x27;2ba481c2-1395-4057-9432-cd96bff4fcfe&amp;#x27;]\n2025-01-08 09:44:20,230 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.experimental.dat\n        File_A hash: b&amp;#x27;\\xa4\\xa2\\xa9\\xa9\\xfb+\\xf8X\\xf4\\x94\\xc4\\xbc\\x07\\x19\\x02J\\xd3\\xd7\\x9c\\xa7Ji\\xcc\\xf4[+\\x176\\xf8\\x98\\x94\\xa2&amp;#x27;\n        File_B hash: b&amp;#x27;\\xa4\\xa2\\xa9\\xa9\\xfb+\\xf8X\\xf4\\x94\\xc4\\xbc\\x07\\x19\\x02J\\xd3\\xd7\\x9c\\xa7Ji\\xcc\\xf4[+\\x176\\xf8\\x98\\x94\\xa2&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_bfactor Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:63 cpptraj -i 2ba481c2-1395-4057-9432-cd96bff4fcfe/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 2ba481c2-1395-4057-9432-cd96bff4fcfe/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:20\n| Available memory: 2.908 GB\n\nINPUT: Reading input from &amp;#x27;2ba481c2-1395-4057-9432-cd96bff4fcfe/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/output.dat byres bfactor]\n    ATOMICFLUCT: calculating B factors over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c/output.dat byres bfactor]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2281.5423 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;B-factors&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  B-factors\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.17%)\nTIME:\t\tTrajectory Process : 0.0219 s ( 92.88%)\nTIME:\t\tAction Post        : 0.0001 s (  0.36%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0013 s (  5.69%)\nTIME:\t\tOther              : 0.0002 s (  0.01%)\nTIME:\tRun Total 0.0236 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0867 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_bfactor_experimental/sandbox_200aade6-28d8-4358-ba72-7a33e1f30a7c&amp;#x27;, &amp;#x27;2ba481c2-1395-4057-9432-cd96bff4fcfe&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_bfactor_experimental/cpptraj_bfactor_experimental_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_convert.py::TestCpptrajConvert::test_convert&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_convert.py::TestCpptrajConvert::test_convert&#34;, &#34;duration&#34;: &#34;596 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_convert.py::TestCpptrajConvert::test_convert&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;596 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:20,717 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_convert Version: 5.0.1\n2025-01-08 09:44:20,717 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853 directory successfully created\n2025-01-08 09:44:20,725 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853\n2025-01-08 09:44:20,737 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853\n2025-01-08 09:44:20,738 [MainThread  ] [INFO ]  cpptraj -i bc612eba-545e-4f69-bfc3-8133e5b2f468/instructions.in\n\n2025-01-08 09:44:20,826 [MainThread  ] [INFO ]  Executing: cpptraj -i bc612eba-545e-4f69-bfc3-8133e5b2f468/instructions.in...\n2025-01-08 09:44:20,826 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:20,827 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:20\n| Available memory: 2.907 GB\n\nINPUT: Reading input from &amp;#x27;bc612eba-545e-4f69-bfc3-8133e5b2f468/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 3837.5931 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.20%)\nTIME:\t\tTrajectory Process : 0.0130 s ( 99.26%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.02%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0131 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0487 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:20,832 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853&amp;#x27;, &amp;#x27;bc612eba-545e-4f69-bfc3-8133e5b2f468&amp;#x27;]\n2025-01-08 09:44:20,833 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_convert/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_convert/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.convert.netcdf\n     SIZE_A: 426420 bytes\n     SIZE_B: 426420 bytes\n     TOLERANCE: 1.0%, Low: 422155.8 bytes, High: 430684.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_convert Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:63 cpptraj -i bc612eba-545e-4f69-bfc3-8133e5b2f468/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:36 Executing: cpptraj -i bc612eba-545e-4f69-bfc3-8133e5b2f468/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:20\n| Available memory: 2.907 GB\n\nINPUT: Reading input from &amp;#x27;bc612eba-545e-4f69-bfc3-8133e5b2f468/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 3837.5931 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.20%)\nTIME:\t\tTrajectory Process : 0.0130 s ( 99.26%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.02%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0131 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0487 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_convert/sandbox_9081eb75-8c0c-466f-9cf9-4de7f65a1853&amp;#x27;, &amp;#x27;bc612eba-545e-4f69-bfc3-8133e5b2f468&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_convert/cpptraj_convert_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_dry.py::TestCpptrajDry::test_dry&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_dry.py::TestCpptrajDry::test_dry&#34;, &#34;duration&#34;: &#34;642 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_dry.py::TestCpptrajDry::test_dry&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;642 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:21,320 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_dry Version: 5.0.1\n2025-01-08 09:44:21,321 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3 directory successfully created\n2025-01-08 09:44:21,331 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3\n2025-01-08 09:44:21,345 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3\n2025-01-08 09:44:21,346 [MainThread  ] [INFO ]  cpptraj -i 7cd765a7-0673-461b-9413-d077e426fa19/instructions.in\n\n2025-01-08 09:44:21,462 [MainThread  ] [INFO ]  Executing: cpptraj -i 7cd765a7-0673-461b-9413-d077e426fa19/instructions.in...\n2025-01-08 09:44:21,464 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:21,464 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:21\n| Available memory: 2.901 GB\n\nINPUT: Reading input from &amp;#x27;7cd765a7-0673-461b-9413-d077e426fa19/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@H*,1H*,2H*,3H*]\n    STRIP: Stripping atoms in mask [!@H*,1H*,2H*,3H*]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (3 actions):\n  0: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  1: [strip !@H*,1H*,2H*,3H*]\n\tStripping 5698 atoms.\n\tStripped topology: 5509 atoms, 710 res, box: None, 5509 mol\n  2: [strip !@CA]\nWarning: Mask [!@CA] would strip all atoms. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 1275.2499 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0392 s ( 99.01%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0004 s (  0.01%)\nTIME:\tRun Total 0.0396 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0745 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:21,478 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3&amp;#x27;, &amp;#x27;7cd765a7-0673-461b-9413-d077e426fa19&amp;#x27;]\n2025-01-08 09:44:21,479 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_dry/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_dry/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.dry.netcdf\n     SIZE_A: 3305820 bytes\n     SIZE_B: 3305820 bytes\n     TOLERANCE: 1.0%, Low: 3272761.8 bytes, High: 3338878.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_dry Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:63 cpptraj -i 7cd765a7-0673-461b-9413-d077e426fa19/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 7cd765a7-0673-461b-9413-d077e426fa19/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:21\n| Available memory: 2.901 GB\n\nINPUT: Reading input from &amp;#x27;7cd765a7-0673-461b-9413-d077e426fa19/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@H*,1H*,2H*,3H*]\n    STRIP: Stripping atoms in mask [!@H*,1H*,2H*,3H*]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (3 actions):\n  0: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  1: [strip !@H*,1H*,2H*,3H*]\n\tStripping 5698 atoms.\n\tStripped topology: 5509 atoms, 710 res, box: None, 5509 mol\n  2: [strip !@CA]\nWarning: Mask [!@CA] would strip all atoms. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 1275.2499 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0392 s ( 99.01%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0004 s (  0.01%)\nTIME:\tRun Total 0.0396 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0745 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_dry/sandbox_17d9335d-55ce-4720-ada4-6390414a0df3&amp;#x27;, &amp;#x27;7cd765a7-0673-461b-9413-d077e426fa19&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_dry/cpptraj_dry_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_image.py::TestCpptrajImage::test_image&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_image.py::TestCpptrajImage::test_image&#34;, &#34;duration&#34;: &#34;603 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_image.py::TestCpptrajImage::test_image&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;603 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:21,962 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_image Version: 5.0.1\n2025-01-08 09:44:21,962 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c directory successfully created\n2025-01-08 09:44:21,971 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c\n2025-01-08 09:44:21,984 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c\n2025-01-08 09:44:21,985 [MainThread  ] [INFO ]  cpptraj -i 80f14082-8446-4ec3-a79b-8365f36f645e/instructions.in\n\n2025-01-08 09:44:22,082 [MainThread  ] [INFO ]  Executing: cpptraj -i 80f14082-8446-4ec3-a79b-8365f36f645e/instructions.in...\n2025-01-08 09:44:22,083 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:22,083 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:22\n| Available memory: 2.896 GB\n\nINPUT: Reading input from &amp;#x27;80f14082-8446-4ec3-a79b-8365f36f645e/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (4 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2101.0169 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0238 s ( 99.53%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.10%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0239 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0581 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:22,089 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c&amp;#x27;, &amp;#x27;80f14082-8446-4ec3-a79b-8365f36f645e&amp;#x27;]\n2025-01-08 09:44:22,090 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_image/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_image/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.image.netcdf\n     SIZE_A: 426420 bytes\n     SIZE_B: 426420 bytes\n     TOLERANCE: 1.0%, Low: 422155.8 bytes, High: 430684.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_image Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:63 cpptraj -i 80f14082-8446-4ec3-a79b-8365f36f645e/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 80f14082-8446-4ec3-a79b-8365f36f645e/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:22\n| Available memory: 2.896 GB\n\nINPUT: Reading input from &amp;#x27;80f14082-8446-4ec3-a79b-8365f36f645e/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (4 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2101.0169 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0238 s ( 99.53%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.10%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0239 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0581 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_image/sandbox_f6992d00-ab99-4ff4-bcc7-157e66c83a1c&amp;#x27;, &amp;#x27;80f14082-8446-4ec3-a79b-8365f36f645e&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_image/cpptraj_image_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_input.py::TestCpptrajInput::test_input&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_input.py::TestCpptrajInput::test_input&#34;, &#34;duration&#34;: &#34;640 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_input.py::TestCpptrajInput::test_input&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;640 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:22,606 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_input Version: 5.0.1\n2025-01-08 09:44:22,607 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_input/sandbox_1d9dc18c-ec07-4c08-ae10-286c56db9e8b directory successfully created\n2025-01-08 09:44:22,608 [MainThread  ] [INFO ]  cpptraj -i cpptraj_input_instructions.in\n\n2025-01-08 09:44:22,733 [MainThread  ] [INFO ]  Executing: cpptraj -i cpptraj_input_instructions.in...\n2025-01-08 09:44:22,734 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:22,734 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:22\n| Available memory: 2.895 GB\n\nINPUT: Reading input from &amp;#x27;cpptraj_input_instructions.in&amp;#x27;\n  [parm /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top]\n\tReading &amp;#x27;/home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd]\n\tReading &amp;#x27;/home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [trajout /tmp/biobb/unitests_2/cpptraj_input/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_input/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_input/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 993.5222 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.03%)\nTIME:\t\tTrajectory Process : 0.0503 s ( 99.85%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0504 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0846 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_input/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_input/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.in.netcdf\n     SIZE_A: 6724620 bytes\n     SIZE_B: 6724620 bytes\n     TOLERANCE: 1.0%, Low: 6657373.8 bytes, High: 6791866.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_input/cpptraj_input_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_input Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_input/cpptraj_input_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_input/sandbox_1d9dc18c-ec07-4c08-ae10-286c56db9e8b directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:63 cpptraj -i cpptraj_input_instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:36 Executing: cpptraj -i cpptraj_input_instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_input/cpptraj_input_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:22\n| Available memory: 2.895 GB\n\nINPUT: Reading input from &amp;#x27;cpptraj_input_instructions.in&amp;#x27;\n  [parm /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top]\n\tReading &amp;#x27;/home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd]\n\tReading &amp;#x27;/home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [trajout /tmp/biobb/unitests_2/cpptraj_input/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_input/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_input/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 993.5222 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.03%)\nTIME:\t\tTrajectory Process : 0.0503 s ( 99.85%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0504 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0846 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_mask.py::TestCpptrajMask::test_mask&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_mask.py::TestCpptrajMask::test_mask&#34;, &#34;duration&#34;: &#34;594 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_mask.py::TestCpptrajMask::test_mask&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;594 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:23,222 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_mask Version: 5.0.1\n2025-01-08 09:44:23,223 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387 directory successfully created\n2025-01-08 09:44:23,232 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387\n2025-01-08 09:44:23,245 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387\n2025-01-08 09:44:23,246 [MainThread  ] [INFO ]  cpptraj -i 58e6ceaf-c73a-47a8-89bb-75e50896416c/instructions.in\n\n2025-01-08 09:44:23,330 [MainThread  ] [INFO ]  Executing: cpptraj -i 58e6ceaf-c73a-47a8-89bb-75e50896416c/instructions.in...\n2025-01-08 09:44:23,331 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:23,331 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:23\n| Available memory: 2.897 GB\n\nINPUT: Reading input from &amp;#x27;58e6ceaf-c73a-47a8-89bb-75e50896416c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 3953.1942 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.09%)\nTIME:\t\tTrajectory Process : 0.0126 s ( 99.38%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0127 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0462 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:23,337 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387&amp;#x27;, &amp;#x27;58e6ceaf-c73a-47a8-89bb-75e50896416c&amp;#x27;]\n2025-01-08 09:44:23,338 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_mask/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_mask/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.mask.netcdf\n     SIZE_A: 426420 bytes\n     SIZE_B: 426420 bytes\n     TOLERANCE: 1.0%, Low: 422155.8 bytes, High: 430684.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_mask Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:63 cpptraj -i 58e6ceaf-c73a-47a8-89bb-75e50896416c/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 58e6ceaf-c73a-47a8-89bb-75e50896416c/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:23\n| Available memory: 2.897 GB\n\nINPUT: Reading input from &amp;#x27;58e6ceaf-c73a-47a8-89bb-75e50896416c/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 3953.1942 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.09%)\nTIME:\t\tTrajectory Process : 0.0126 s ( 99.38%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0127 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0462 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_mask/sandbox_4986e4dc-56c2-4e81-8797-73354e195387&amp;#x27;, &amp;#x27;58e6ceaf-c73a-47a8-89bb-75e50896416c&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_mask/cpptraj_mask_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rgyr.py::TestCpptrajRgyr::test_rgyr&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rgyr.py::TestCpptrajRgyr::test_rgyr&#34;, &#34;duration&#34;: &#34;596 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rgyr.py::TestCpptrajRgyr::test_rgyr&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;596 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:23,822 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rgyr Version: 5.0.1\n2025-01-08 09:44:23,822 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676 directory successfully created\n2025-01-08 09:44:23,831 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676\n2025-01-08 09:44:23,843 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676\n2025-01-08 09:44:23,844 [MainThread  ] [INFO ]  cpptraj -i 79424886-2940-403d-9425-e76a8e27106e/instructions.in\n\n2025-01-08 09:44:23,933 [MainThread  ] [INFO ]  Executing: cpptraj -i 79424886-2940-403d-9425-e76a8e27106e/instructions.in...\n2025-01-08 09:44:23,934 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:23,934 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:23\n| Available memory: 2.897 GB\n\nINPUT: Reading input from &amp;#x27;79424886-2940-403d-9425-e76a8e27106e/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [radgyr time 1 out /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/output.dat]\n    RADGYR: Calculating for atoms in mask *.\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [radgyr time 1 out /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/output.dat]\n\t* (710 atoms).\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2942.7344 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRoG_00002 &amp;quot;RoG_00002&amp;quot; (double), size is 50 (0.400 kB)\n\tRoG_00002[Max] &amp;quot;RoG_00002[Max]&amp;quot; (double), size is 50 (0.400 kB)\n    Total data set memory usage is at least 1.200 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RoG_00002 RoG_00002[Max]\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0170 s ( 97.49%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0004 s (  2.13%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0174 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0513 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:23,939 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676&amp;#x27;, &amp;#x27;79424886-2940-403d-9425-e76a8e27106e&amp;#x27;]\n2025-01-08 09:44:23,940 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rgyr/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rgyr/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat\n        File_A hash: b&amp;#x27;\\t\\xc9\\xcd\\xa6\\xf1l\\xdf\\x18\\xe3\\x8b\\x81\\x07\\x08\\x16d#S*\\xa6DF\\x94\\x1b^\\xfcz\\xeb\\xfe]\\xf5c5&amp;#x27;\n        File_B hash: b&amp;#x27;\\t\\xc9\\xcd\\xa6\\xf1l\\xdf\\x18\\xe3\\x8b\\x81\\x07\\x08\\x16d#S*\\xa6DF\\x94\\x1b^\\xfcz\\xeb\\xfe]\\xf5c5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rgyr Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:63 cpptraj -i 79424886-2940-403d-9425-e76a8e27106e/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 79424886-2940-403d-9425-e76a8e27106e/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:23\n| Available memory: 2.897 GB\n\nINPUT: Reading input from &amp;#x27;79424886-2940-403d-9425-e76a8e27106e/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [radgyr time 1 out /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/output.dat]\n    RADGYR: Calculating for atoms in mask *.\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [radgyr time 1 out /tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676/output.dat]\n\t* (710 atoms).\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2942.7344 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRoG_00002 &amp;quot;RoG_00002&amp;quot; (double), size is 50 (0.400 kB)\n\tRoG_00002[Max] &amp;quot;RoG_00002[Max]&amp;quot; (double), size is 50 (0.400 kB)\n    Total data set memory usage is at least 1.200 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RoG_00002 RoG_00002[Max]\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.07%)\nTIME:\t\tTrajectory Process : 0.0170 s ( 97.49%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0004 s (  2.13%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0174 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0513 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rgyr/sandbox_e115d70c-24d5-4726-96f1-a3380e3ca676&amp;#x27;, &amp;#x27;79424886-2940-403d-9425-e76a8e27106e&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rgyr/cpptraj_rgyr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsFirst::test_rms_first&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsFirst::test_rms_first&#34;, &#34;duration&#34;: &#34;668 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsFirst::test_rms_first&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;668 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:24,412 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\n2025-01-08 09:44:24,413 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1 directory successfully created\n2025-01-08 09:44:24,422 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1\n2025-01-08 09:44:24,435 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1\n2025-01-08 09:44:24,436 [MainThread  ] [INFO ]  cpptraj -i 11d55e99-309f-420c-ae53-9c56ba4104d0/instructions.in\n\n2025-01-08 09:44:24,603 [MainThread  ] [INFO ]  Executing: cpptraj -i 11d55e99-309f-420c-ae53-9c56ba4104d0/instructions.in...\n2025-01-08 09:44:24,604 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:24,605 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:24\n| Available memory: 2.896 GB\n\nINPUT: Reading input from &amp;#x27;11d55e99-309f-420c-ae53-9c56ba4104d0/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first out /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.dat]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first out /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.dat]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 556.9976 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00002\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.02%)\nTIME:\t\tTrajectory Process : 0.0898 s ( 99.61%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0003 s (  0.28%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0901 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1272 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:24,612 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1&amp;#x27;, &amp;#x27;11d55e99-309f-420c-ae53-9c56ba4104d0&amp;#x27;]\n2025-01-08 09:44:24,613 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rms_first/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rms_first/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.dat\n        File_A hash: b&amp;#x27;b\\x15\\x8a\\x17\\xa1\\\\\\xb7{\\x98\\xfc\\x8dx\\xc5Sz)4P\\xe0D\\xee@\\xc3rQ\\xf26n\\x99\\xe1\\\\=&amp;#x27;\n        File_B hash: b&amp;#x27;b\\x15\\x8a\\x17\\xa1\\\\\\xb7{\\x98\\xfc\\x8dx\\xc5Sz)4P\\xe0D\\xee@\\xc3rQ\\xf26n\\x99\\xe1\\\\=&amp;#x27;\nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rms_first/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_rms_first/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.netcdf\n     SIZE_A: 862731 bytes\n     SIZE_B: 862731 bytes\n     TOLERANCE: 1.0%, Low: 854103.69 bytes, High: 871358.31 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:63 cpptraj -i 11d55e99-309f-420c-ae53-9c56ba4104d0/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 11d55e99-309f-420c-ae53-9c56ba4104d0/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:24\n| Available memory: 2.896 GB\n\nINPUT: Reading input from &amp;#x27;11d55e99-309f-420c-ae53-9c56ba4104d0/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first out /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.dat]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first out /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.dat]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 556.9976 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00002\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.02%)\nTIME:\t\tTrajectory Process : 0.0898 s ( 99.61%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0003 s (  0.28%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0901 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1272 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_first/sandbox_5d41d509-8284-40b3-b019-9547f71b61f1&amp;#x27;, &amp;#x27;11d55e99-309f-420c-ae53-9c56ba4104d0&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_first/cpptraj_rms_first_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsAverage::test_rms_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsAverage::test_rms_average&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsAverage::test_rms_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:25,113 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\n2025-01-08 09:44:25,114 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae directory successfully created\n2025-01-08 09:44:25,123 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae\n2025-01-08 09:44:25,135 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae\n2025-01-08 09:44:25,136 [MainThread  ] [INFO ]  cpptraj -i 96e22d56-97f4-447f-a1a3-753901071ba2/instructions.in\n\n2025-01-08 09:44:26,306 [MainThread  ] [INFO ]  Executing: cpptraj -i 96e22d56-97f4-447f-a1a3-753901071ba2/instructions.in...\n2025-01-08 09:44:26,307 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:26,308 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:25\n| Available memory: 2.895 GB\n\nINPUT: Reading input from &amp;#x27;96e22d56-97f4-447f-a1a3-753901071ba2/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2176.3733 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0230 s ( 98.42%)\nTIME:\t\tAction Post        : 0.0003 s (  1.09%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.11%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0233 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA out /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.dat]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [rms ref MyAvg @CA out /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 46.5408 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00003\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.00%)\nTIME:\t\tTrajectory Process : 1.0743 s ( 99.96%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0003 s (  0.03%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 1.0747 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 1.1320 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:26,342 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae&amp;#x27;, &amp;#x27;96e22d56-97f4-447f-a1a3-753901071ba2&amp;#x27;]\n2025-01-08 09:44:26,343 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rms_average/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rms_average/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.average.dat\n        File_A hash: b&amp;#x27;\\xd9\\xbf\\x08bIk\\xd1\\x89X\\xec\\x95#&amp;quot;\\xda\\xb6\\xf1\\xb9\\xd4\\\\\\x80\\xfe\\xaef\\x16\\xf85\\x9f(\\x8a\\xa3\\xbbQ&amp;#x27;\n        File_B hash: b&amp;#x27;\\xd9\\xbf\\x08bIk\\xd1\\x89X\\xec\\x95#&amp;quot;\\xda\\xb6\\xf1\\xb9\\xd4\\\\\\x80\\xfe\\xaef\\x16\\xf85\\x9f(\\x8a\\xa3\\xbbQ&amp;#x27;\nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rms_average/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_rms_average/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.average.netcdf\n     SIZE_A: 13616631 bytes\n     SIZE_B: 13616631 bytes\n     TOLERANCE: 1.0%, Low: 13480464.69 bytes, High: 13752797.31 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:63 cpptraj -i 96e22d56-97f4-447f-a1a3-753901071ba2/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 96e22d56-97f4-447f-a1a3-753901071ba2/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:25\n| Available memory: 2.895 GB\n\nINPUT: Reading input from &amp;#x27;96e22d56-97f4-447f-a1a3-753901071ba2/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2176.3733 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0230 s ( 98.42%)\nTIME:\t\tAction Post        : 0.0003 s (  1.09%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.11%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0233 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA out /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.dat]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [rms ref MyAvg @CA out /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 46.5408 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00003\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.00%)\nTIME:\t\tTrajectory Process : 1.0743 s ( 99.96%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0003 s (  0.03%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 1.0747 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 1.1320 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_average/sandbox_bdfb7ad5-fd09-4103-8120-d4e7adf96dae&amp;#x27;, &amp;#x27;96e22d56-97f4-447f-a1a3-753901071ba2&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_average/cpptraj_rms_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsExperimental::test_rms_experimental&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsExperimental::test_rms_experimental&#34;, &#34;duration&#34;: &#34;722 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rms.py::TestCpptrajRmsExperimental::test_rms_experimental&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;722 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:26,836 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\n2025-01-08 09:44:26,837 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011 directory successfully created\n2025-01-08 09:44:26,847 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011\n2025-01-08 09:44:26,861 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011\n2025-01-08 09:44:26,863 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011\n2025-01-08 09:44:26,864 [MainThread  ] [INFO ]  cpptraj -i e00172ca-df33-4f3a-ba78-091f49a108e8/instructions.in\n\n2025-01-08 09:44:27,063 [MainThread  ] [INFO ]  Executing: cpptraj -i e00172ca-df33-4f3a-ba78-091f49a108e8/instructions.in...\n2025-01-08 09:44:27,064 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:27,065 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:26\n| Available memory: 2.908 GB\n\nINPUT: Reading input from &amp;#x27;e00172ca-df33-4f3a-ba78-091f49a108e8/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA out /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.dat]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA out /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 512.6260 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00004\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0975 s ( 99.24%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0003 s (  0.33%)\nTIME:\t\tOther              : 0.0004 s (  0.00%)\nTIME:\tRun Total 0.0983 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1600 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:27,072 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011&amp;#x27;, &amp;#x27;e00172ca-df33-4f3a-ba78-091f49a108e8&amp;#x27;]\n2025-01-08 09:44:27,073 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rms_experimental/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rms_experimental/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.experimental.dat\n        File_A hash: b&amp;#x27;\\x84\\xe9\\x89\\xf1!\\xb6e\\x9d\\x8b\\x15\\n\\xe5y\\x0f\\x01Hv3\\xe6\\x90\\x8e\\xe2|\\xc4:4\\xd7\\xf8\\xc0\\x06\\xc8m&amp;#x27;\n        File_B hash: b&amp;#x27;\\x84\\xe9\\x89\\xf1!\\xb6e\\x9d\\x8b\\x15\\n\\xe5y\\x0f\\x01Hv3\\xe6\\x90\\x8e\\xe2|\\xc4:4\\xd7\\xf8\\xc0\\x06\\xc8m&amp;#x27;\nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rms_experimental/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_rms_experimental/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.experimental.netcdf\n     SIZE_A: 862731 bytes\n     SIZE_B: 862731 bytes\n     TOLERANCE: 1.0%, Low: 854103.69 bytes, High: 871358.31 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:63 cpptraj -i e00172ca-df33-4f3a-ba78-091f49a108e8/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:36 Executing: cpptraj -i e00172ca-df33-4f3a-ba78-091f49a108e8/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:26\n| Available memory: 2.908 GB\n\nINPUT: Reading input from &amp;#x27;e00172ca-df33-4f3a-ba78-091f49a108e8/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA out /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.dat]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [trajout /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.netcdf]\nWarning: Format not specified and extension &amp;#x27;.netcdf&amp;#x27; not recognized. Defaulting to Amber Trajectory.\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.netcdf&amp;#x27; as Amber Trajectory\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is an AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA out /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.dat]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 512.6260 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (2 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.800 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  RMSD_00004\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.05%)\nTIME:\t\tTrajectory Process : 0.0975 s ( 99.24%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0003 s (  0.33%)\nTIME:\t\tOther              : 0.0004 s (  0.00%)\nTIME:\tRun Total 0.0983 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1600 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rms_experimental/sandbox_783aa324-8e75-493b-b504-cc1130955011&amp;#x27;, &amp;#x27;e00172ca-df33-4f3a-ba78-091f49a108e8&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rms_experimental/cpptraj_rms_experimental_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfFirst::test_rmsf_first&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfFirst::test_rmsf_first&#34;, &#34;duration&#34;: &#34;616 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfFirst::test_rmsf_first&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;616 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:27,568 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\n2025-01-08 09:44:27,569 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022 directory successfully created\n2025-01-08 09:44:27,577 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022\n2025-01-08 09:44:27,590 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022\n2025-01-08 09:44:27,591 [MainThread  ] [INFO ]  cpptraj -i 5d0d0499-f10b-479a-87da-4a71af62caa1/instructions.in\n\n2025-01-08 09:44:27,689 [MainThread  ] [INFO ]  Executing: cpptraj -i 5d0d0499-f10b-479a-87da-4a71af62caa1/instructions.in...\n2025-01-08 09:44:27,690 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:27,690 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:27\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;5d0d0499-f10b-479a-87da-4a71af62caa1/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2710.7617 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0184 s ( 91.95%)\nTIME:\t\tAction Post        : 0.0002 s (  0.78%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0013 s (  6.69%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0201 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0569 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:27,695 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022&amp;#x27;, &amp;#x27;5d0d0499-f10b-479a-87da-4a71af62caa1&amp;#x27;]\n2025-01-08 09:44:27,697 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rmsf_first/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rmsf_first/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.first.dat\n        File_A hash: b&amp;#x27;\\xe2\\xb6\\x11\\xbc\\xc7\\x9dl\\xb4_\\xb8\\x8e\\x1e^0U\\x00U\\xdaf\\x90\\xac\\xf6\\xd1:\\x0c\\x0c\\xac\\x02m\\xf2\\x01\\t&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe2\\xb6\\x11\\xbc\\xc7\\x9dl\\xb4_\\xb8\\x8e\\x1e^0U\\x00U\\xdaf\\x90\\xac\\xf6\\xd1:\\x0c\\x0c\\xac\\x02m\\xf2\\x01\\t&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:63 cpptraj -i 5d0d0499-f10b-479a-87da-4a71af62caa1/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 5d0d0499-f10b-479a-87da-4a71af62caa1/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:27\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;5d0d0499-f10b-479a-87da-4a71af62caa1/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [rms first]\n    RMSD: (*), reference is first frame (*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms first]\n\tTarget mask: [*](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [*](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2710.7617 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00002 &amp;quot;RMSD_00002&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00003 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.06%)\nTIME:\t\tTrajectory Process : 0.0184 s ( 91.95%)\nTIME:\t\tAction Post        : 0.0002 s (  0.78%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0013 s (  6.69%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0201 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0569 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_first/sandbox_07c92979-aae9-4e1e-8f3a-cde1ebf74022&amp;#x27;, &amp;#x27;5d0d0499-f10b-479a-87da-4a71af62caa1&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_first/cpptraj_rmsf_first_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfAverage::test_rmsf_average&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfAverage::test_rmsf_average&#34;, &#34;duration&#34;: &#34;654 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfAverage::test_rmsf_average&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;654 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:28,208 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\n2025-01-08 09:44:28,209 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2 directory successfully created\n2025-01-08 09:44:28,219 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2\n2025-01-08 09:44:28,231 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2\n2025-01-08 09:44:28,233 [MainThread  ] [INFO ]  cpptraj -i ed17893e-5d97-46a4-8298-081af6a75a5a/instructions.in\n\n2025-01-08 09:44:28,349 [MainThread  ] [INFO ]  Executing: cpptraj -i ed17893e-5d97-46a4-8298-081af6a75a5a/instructions.in...\n2025-01-08 09:44:28,350 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:28,350 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:28\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;ed17893e-5d97-46a4-8298-081af6a75a5a/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2849.8148 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.08%)\nTIME:\t\tTrajectory Process : 0.0175 s ( 97.62%)\nTIME:\t\tAction Post        : 0.0003 s (  1.63%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.16%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0180 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/output.dat byres]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 4184.1004 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.16%)\nTIME:\t\tTrajectory Process : 0.0120 s ( 81.17%)\nTIME:\t\tAction Post        : 0.0014 s (  9.61%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0013 s (  8.93%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0147 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0710 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:28,355 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2&amp;#x27;, &amp;#x27;ed17893e-5d97-46a4-8298-081af6a75a5a&amp;#x27;]\n2025-01-08 09:44:28,356 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rmsf_average/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rmsf_average/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.average.dat\n        File_A hash: b&amp;#x27;\\x0f\\xef\\x87\\xe6\\x0c\\xed\\xf4s\\xdf\\xf50\\x01X;\\xab@\\xcb\\xcd\\xb6\\xf5R\\x9b\\xdaI\\x85\\xb2\\xae\\xa5\\x9c\\xe1\\xe5\\xfc&amp;#x27;\n        File_B hash: b&amp;#x27;\\x0f\\xef\\x87\\xe6\\x0c\\xed\\xf4s\\xdf\\xf50\\x01X;\\xab@\\xcb\\xcd\\xb6\\xf5R\\x9b\\xdaI\\x85\\xb2\\xae\\xa5\\x9c\\xe1\\xe5\\xfc&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:63 cpptraj -i ed17893e-5d97-46a4-8298-081af6a75a5a/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:36 Executing: cpptraj -i ed17893e-5d97-46a4-8298-081af6a75a5a/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:28\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;ed17893e-5d97-46a4-8298-081af6a75a5a/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [average crdset MyAvg]\n\tSetting active reference for distance-based masks: &amp;#x27;MyAvg&amp;#x27;\n    AVERAGE: Averaging over coordinates in mask [*]\n\tStart: 1  Stop: Final frame\n\tSaving averaged coords to set &amp;#x27;MyAvg&amp;#x27;\n  [run]\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (6 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [average crdset MyAvg]\n\tMask [*] corresponds to 710 atoms.\n\tAveraging over 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2849.8148 frames / second.\n\nACTION OUTPUT:\n    AVERAGE: 50 frames, COORDS set &amp;#x27;MyAvg&amp;#x27;\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (1 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n    Total data set memory usage is at least 0.400 kB\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.08%)\nTIME:\t\tTrajectory Process : 0.0175 s ( 97.62%)\nTIME:\t\tAction Post        : 0.0003 s (  1.63%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.16%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0180 s\n---------- RUN END ---------------------------------------------------\n  [rms ref MyAvg @CA]\n    RMSD: (@CA), reference is &amp;quot;MyAvg&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: MyAvg\n\tActive reference frame for distance-based masks is &amp;#x27;MyAvg&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (2 actions):\n  0: [rms ref MyAvg @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [@CA](710)\n  1: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2/output.dat byres]\n\tMask [*] corresponds to 11207 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 4184.1004 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00003 &amp;quot;RMSD_00003&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00004 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.16%)\nTIME:\t\tTrajectory Process : 0.0120 s ( 81.17%)\nTIME:\t\tAction Post        : 0.0014 s (  9.61%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0013 s (  8.93%)\nTIME:\t\tOther              : 0.0000 s (  0.00%)\nTIME:\tRun Total 0.0147 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0710 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_average/sandbox_2c45cb2e-8ded-4f9b-b54c-55f217a7f1d2&amp;#x27;, &amp;#x27;ed17893e-5d97-46a4-8298-081af6a75a5a&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_average/cpptraj_rmsf_average_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfExperimental::test_rmsf_experimental&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfExperimental::test_rmsf_experimental&#34;, &#34;duration&#34;: &#34;635 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_rmsf.py::TestCpptrajRmsfExperimental::test_rmsf_experimental&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;635 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:28,842 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\n2025-01-08 09:44:28,843 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7 directory successfully created\n2025-01-08 09:44:28,851 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7\n2025-01-08 09:44:28,864 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7\n2025-01-08 09:44:28,866 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7\n2025-01-08 09:44:28,867 [MainThread  ] [INFO ]  cpptraj -i a539d10c-19c7-4d00-9fba-ab1bb5345833/instructions.in\n\n2025-01-08 09:44:28,989 [MainThread  ] [INFO ]  Executing: cpptraj -i a539d10c-19c7-4d00-9fba-ab1bb5345833/instructions.in...\n2025-01-08 09:44:28,990 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:28,990 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:28\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;a539d10c-19c7-4d00-9fba-ab1bb5345833/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2777.3149 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.22%)\nTIME:\t\tTrajectory Process : 0.0180 s ( 92.13%)\nTIME:\t\tAction Post        : 0.0001 s (  0.45%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0013 s (  6.88%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0195 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0820 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:28,995 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7&amp;#x27;, &amp;#x27;a539d10c-19c7-4d00-9fba-ab1bb5345833&amp;#x27;]\n2025-01-08 09:44:28,997 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/output.dat\n        File_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.experimental.dat\n        File_A hash: b&amp;#x27;\\xcb1@\\xbf\\x15I\\xb7xM{\\x85\\x03\\xbc\\xd4\\xfd\\xde\\x11\\x8d\\x1c\\xffj\\xe3]\\xb5!\\xb6C\\x7fMV\\xa0\\xc6&amp;#x27;\n        File_B hash: b&amp;#x27;\\xcb1@\\xbf\\x15I\\xb7xM{\\x85\\x03\\xbc\\xd4\\xfd\\xde\\x11\\x8d\\x1c\\xffj\\xe3]\\xb5!\\xb6C\\x7fMV\\xa0\\xc6&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_rmsf Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb to /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:63 cpptraj -i a539d10c-19c7-4d00-9fba-ab1bb5345833/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:36 Executing: cpptraj -i a539d10c-19c7-4d00-9fba-ab1bb5345833/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:28\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;a539d10c-19c7-4d00-9fba-ab1bb5345833/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [center !@H*,1H*,2H*,3H* origin]\n    CENTER: Centering coordinates using geometric center of atoms in mask (!@H*,1H*,2H*,3H*) to\n\tcoordinate origin.\n  [autoimage]\n    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.\n  [rms first !@H*,1H*,2H*,3H*]\n    RMSD: (!@H*,1H*,2H*,3H*), reference is first frame (!@H*,1H*,2H*,3H*).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n    STRIP: Stripping atoms in mask [:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [parm /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb noconect [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb&amp;#x27; as PDB File\n\tNot reading bond info from CONECT records.\n\tNot reading bond info from LINK records.\n\tDetermining bond info from distances.\nWarning: Determining bond length parameters from element types for &amp;#x27;experimental.1e5t.pdb&amp;#x27;.\n  [reference /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb !:WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K parm [exp]]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/experimental.1e5t.pdb&amp;#x27; as PDB\n\tRead CRYST1 info from PDB: a=70.7 b=99.7 c=110.9 alpha=90 beta=90 gamma=90\n\tStripped ref parm: 5752 atoms, 719 res, box: None, 10 mol\n\tSetting active reference for distance-based masks: &amp;#x27;experimental.1e5t.pdb&amp;#x27;\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;cpptraj.parm.top&amp;#x27; has 11207.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\nWarning: Active reference has only 5752 atoms, parm &amp;#x27;experimental.1e5t.pdb&amp;#x27; has 6618.\nWarning: Parm will only have reference coordinates for the first 5752 atoms (distance-based masks only).\n  [rms reference @CA]\n    RMSD: (@CA), reference is &amp;quot;experimental.1e5t.pdb:1&amp;quot; (@CA).\n\tBest-fit RMSD will be calculated, coords will be rotated and translated.\n  [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/output.dat byres]\n    ATOMICFLUCT: calculating atomic positional fluctuations over residues.\n\tOutput to file /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/output.dat\n\tAtom mask: [*]\n\tStart: 1  Stop: Final frame\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (2 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n 1: [exp] experimental.1e5t.pdb, 6618 atoms, 1585 res, box: None, 876 mol, 866 solvent\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nREFERENCE FRAMES (1 total):\n    0: experimental.1e5t.pdb:1\n\tActive reference frame for distance-based masks is &amp;#x27;experimental.1e5t.pdb:1&amp;#x27;\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (7 actions):\n  0: [center !@H*,1H*,2H*,3H* origin]\n\tMask [!@H*,1H*,2H*,3H*] corresponds to 5698 atoms.\n  1: [autoimage]\nWarning: Topology cpptraj.parm.top does not contain box information.\nWarning: Setup incomplete for [autoimage]: Skipping\n  2: [rms first !@H*,1H*,2H*,3H*]\n\tTarget mask: [!@H*,1H*,2H*,3H*](5698)\n\tReference topology: cpptraj.parm.top\n\tReference mask: [!@H*,1H*,2H*,3H*](5698)\n  3: [strip :WAT,HOH,SOL,TIP3,TP3,SOD,CLA,Na+,Cl-,NA,CL,K+,K]\n\tStripping 0 atoms.\nWarning: No atoms to strip. Skipping.\nWarning: Setup incomplete for [strip]: Skipping\n  4: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n  5: [rms reference @CA]\n\tTarget mask: [@CA](710)\n\tReference topology: experimental.1e5t.pdb\n\tReference mask: [@CA](710)\n  6: [atomicfluct out /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7/output.dat byres]\n\tMask [*] corresponds to 710 atoms.\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 2777.3149 frames / second.\n\nACTION OUTPUT:\n    ATOMICFLUCT: Calculating fluctuations for 50 sets.\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (3 total):\n\tRMSD_00001 &amp;quot;RMSD_00001&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tRMSD_00004 &amp;quot;RMSD_00004&amp;quot; (double, rms), size is 50 (0.400 kB)\n\tFluct_00005 &amp;quot;AtomicFlx&amp;quot; (X-Y mesh), size is 710 (11.360 kB)\n    Total data set memory usage is at least 12.160 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  AtomicFlx\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.22%)\nTIME:\t\tTrajectory Process : 0.0180 s ( 92.13%)\nTIME:\t\tAction Post        : 0.0001 s (  0.45%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0013 s (  6.88%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0195 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0820 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_rmsf_experimental/sandbox_16556af5-212d-42e9-b0b0-69162438cdc7&amp;#x27;, &amp;#x27;a539d10c-19c7-4d00-9fba-ab1bb5345833&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_rmsf_experimental/cpptraj_rmsf_experimental_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_slice.py::TestCpptrajSlice::test_slice&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_slice.py::TestCpptrajSlice::test_slice&#34;, &#34;duration&#34;: &#34;588 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_slice.py::TestCpptrajSlice::test_slice&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;588 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:29,478 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_slice Version: 5.0.1\n2025-01-08 09:44:29,478 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c directory successfully created\n2025-01-08 09:44:29,487 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c\n2025-01-08 09:44:29,499 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c\n2025-01-08 09:44:29,500 [MainThread  ] [INFO ]  cpptraj -i a6bfabce-064c-435d-aa2b-d413ea61de8e/instructions.in\n\n2025-01-08 09:44:29,584 [MainThread  ] [INFO ]  Executing: cpptraj -i a6bfabce-064c-435d-aa2b-d413ea61de8e/instructions.in...\n2025-01-08 09:44:29,586 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:29,586 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:29\n| Available memory: 2.902 GB\n\nINPUT: Reading input from &amp;#x27;a6bfabce-064c-435d-aa2b-d413ea61de8e/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.traj.dcd 2 20 2]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 10 of 50)\n  Coordinate processing will occur on 10 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (10 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (2-20, 2) -----\n 0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.\n\nRead 10 frames and processed 10 frames.\nTIME: Avg. throughput= 1513.0882 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.21%)\nTIME:\t\tTrajectory Process : 0.0066 s ( 98.80%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0067 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0438 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:29,591 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c&amp;#x27;, &amp;#x27;a6bfabce-064c-435d-aa2b-d413ea61de8e&amp;#x27;]\n2025-01-08 09:44:29,592 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_slice/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_slice/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.slice.netcdf\n     SIZE_A: 85620 bytes\n     SIZE_B: 85620 bytes\n     TOLERANCE: 1.0%, Low: 84763.8 bytes, High: 86476.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_slice Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:63 cpptraj -i a6bfabce-064c-435d-aa2b-d413ea61de8e/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:36 Executing: cpptraj -i a6bfabce-064c-435d-aa2b-d413ea61de8e/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:29\n| Available memory: 2.902 GB\n\nINPUT: Reading input from &amp;#x27;a6bfabce-064c-435d-aa2b-d413ea61de8e/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.traj.dcd 2 20 2]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 10 of 50)\n  Coordinate processing will occur on 10 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (10 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (2-20, 2) -----\n 0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.\n\nRead 10 frames and processed 10 frames.\nTIME: Avg. throughput= 1513.0882 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.21%)\nTIME:\t\tTrajectory Process : 0.0066 s ( 98.80%)\nTIME:\t\tAction Post        : 0.0000 s (  0.01%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.01%)\nTIME:\t\tData File Write    : 0.0000 s (  0.01%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0067 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0438 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_slice/sandbox_39499448-c6f0-4d07-9c4d-717183b9146c&amp;#x27;, &amp;#x27;a6bfabce-064c-435d-aa2b-d413ea61de8e&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_slice/cpptraj_slice_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_snapshot.py::TestCpptrajSnapshot::test_snapshot&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_snapshot.py::TestCpptrajSnapshot::test_snapshot&#34;, &#34;duration&#34;: &#34;709 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_snapshot.py::TestCpptrajSnapshot::test_snapshot&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;709 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:30,056 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_snapshot Version: 5.0.1\n2025-01-08 09:44:30,057 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c directory successfully created\n2025-01-08 09:44:30,065 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c\n2025-01-08 09:44:30,076 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c\n2025-01-08 09:44:30,077 [MainThread  ] [INFO ]  cpptraj -i 0033a016-9396-457f-88e4-8aa986d51f41/instructions.in\n\n2025-01-08 09:44:30,154 [MainThread  ] [INFO ]  Executing: cpptraj -i 0033a016-9396-457f-88e4-8aa986d51f41/instructions.in...\n2025-01-08 09:44:30,155 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:30,155 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:30\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;0033a016-9396-457f-88e4-8aa986d51f41/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.traj.dcd 12 12 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/output.pdb&amp;#x27; as PDB\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 1 of 50)\n  Coordinate processing will occur on 1 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.pdb&amp;#x27; (1 frames) is a PDB file\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/output.pdb (coordinates)\n----- cpptraj.traj.dcd (12-12, 1) -----\n100% Complete.\n\nRead 1 frames and processed 1 frames.\nTIME: Avg. throughput= 189.3222 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.24%)\nTIME:\t\tTrajectory Process : 0.0053 s ( 98.32%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.04%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0054 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0394 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:30,160 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c&amp;#x27;, &amp;#x27;0033a016-9396-457f-88e4-8aa986d51f41&amp;#x27;]\n2025-01-08 09:44:30,161 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_snapshot/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_2/cpptraj_snapshot/output.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.snapshot.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 710\n     Atoms ALIGNED in PDB_B: 710\n     RMS: 1.822347074775497e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_snapshot Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:63 cpptraj -i 0033a016-9396-457f-88e4-8aa986d51f41/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 0033a016-9396-457f-88e4-8aa986d51f41/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:30\n| Available memory: 2.903 GB\n\nINPUT: Reading input from &amp;#x27;0033a016-9396-457f-88e4-8aa986d51f41/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.traj.dcd 12 12 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip !@CA]\n    STRIP: Stripping atoms in mask [!@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/output.pdb pdb]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/output.pdb&amp;#x27; as PDB\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 1 of 50)\n  Coordinate processing will occur on 1 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.pdb&amp;#x27; (1 frames) is a PDB file\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip !@CA]\n\tStripping 10497 atoms.\n\tStripped topology: 710 atoms, 710 res, box: None, 710 mol\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c/output.pdb (coordinates)\n----- cpptraj.traj.dcd (12-12, 1) -----\n100% Complete.\n\nRead 1 frames and processed 1 frames.\nTIME: Avg. throughput= 189.3222 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.24%)\nTIME:\t\tTrajectory Process : 0.0053 s ( 98.32%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.04%)\nTIME:\t\tOther              : 0.0001 s (  0.01%)\nTIME:\tRun Total 0.0054 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0394 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_snapshot/sandbox_ac96b976-5aa5-4c65-a752-8f4fb1552c3c&amp;#x27;, &amp;#x27;0033a016-9396-457f-88e4-8aa986d51f41&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_snapshot/cpptraj_snapshot_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_strip.py::TestCpptrajStrip::test_strip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_strip.py::TestCpptrajStrip::test_strip&#34;, &#34;duration&#34;: &#34;669 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_ambertools/test_cpptraj_strip.py::TestCpptrajStrip::test_strip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;669 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:30,817 [MainThread  ] [INFO ]  Module: biobb_analysis.ambertools.cpptraj_strip Version: 5.0.1\n2025-01-08 09:44:30,818 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033 directory successfully created\n2025-01-08 09:44:30,826 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033\n2025-01-08 09:44:30,838 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033\n2025-01-08 09:44:30,839 [MainThread  ] [INFO ]  cpptraj -i dc62adab-8b59-4ba5-b892-58d510bf15cc/instructions.in\n\n2025-01-08 09:44:30,962 [MainThread  ] [INFO ]  Executing: cpptraj -i dc62adab-8b59-4ba5-b892-58d510bf15cc/instructions.in...\n2025-01-08 09:44:30,963 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:30,963 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:30\n| Available memory: 2.892 GB\n\nINPUT: Reading input from &amp;#x27;dc62adab-8b59-4ba5-b892-58d510bf15cc/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip @CA]\n    STRIP: Stripping atoms in mask [@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip @CA]\n\tStripping 710 atoms.\n\tStripped topology: 10497 atoms, 710 res, box: None, 2100 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 966.5758 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.02%)\nTIME:\t\tTrajectory Process : 0.0517 s ( 98.78%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0006 s (  0.01%)\nTIME:\tRun Total 0.0524 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0861 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\n2025-01-08 09:44:30,980 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033&amp;#x27;, &amp;#x27;dc62adab-8b59-4ba5-b892-58d510bf15cc&amp;#x27;]\n2025-01-08 09:44:30,981 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/cpptraj_strip/output.netcdf\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/cpptraj_strip/output.netcdf\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/ambertools/ref_cpptraj.strip.netcdf\n     SIZE_A: 6298620 bytes\n     SIZE_B: 6298620 bytes\n     TOLERANCE: 1.0%, Low: 6235633.8 bytes, High: 6361606.2 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Module: biobb_analysis.ambertools.cpptraj_strip Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:82 /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033 directory successfully created\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.parm.top to /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd to /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:63 cpptraj -i dc62adab-8b59-4ba5-b892-58d510bf15cc/instructions.in\n\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:36 Executing: cpptraj -i dc62adab-8b59-4ba5-b892-58d510bf15cc/instructions.in...\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 01/08/25 09:44:30\n| Available memory: 2.892 GB\n\nINPUT: Reading input from &amp;#x27;dc62adab-8b59-4ba5-b892-58d510bf15cc/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.parm.top]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.parm.top&amp;#x27; as Amber Topology\n\tThis Amber topology does not include atomic numbers.\n\tAssigning elements from atom masses/names.\n\tNo SCEE section: setting Amber default (1.2)\n\tNo SCNB section: setting Amber default (2.0)\n  [trajin /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.traj.dcd 1 -1 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/cpptraj.traj.dcd&amp;#x27; as Charmm DCD\n  [strip @CA]\n    STRIP: Stripping atoms in mask [@CA]\n  [trajout /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/output.netcdf netcdf]\n\tWriting &amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/output.netcdf&amp;#x27; as Amber NetCDF\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: cpptraj.parm.top, 11207 atoms, 710 res, box: None, 1 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;cpptraj.traj.dcd&amp;#x27; is a CHARMM DCD file (coords) Little Endian 32 bit, Parm cpptraj.parm.top (reading 50 of 50)\n  Coordinate processing will occur on 50 frames.\n\nOUTPUT TRAJECTORIES (1 total):\n  &amp;#x27;output.netcdf&amp;#x27; (50 frames) is a NetCDF (NetCDF3) AMBER trajectory\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;cpptraj.parm.top&amp;#x27; (1 actions):\n  0: [strip @CA]\n\tStripping 710 atoms.\n\tStripped topology: 10497 atoms, 710 res, box: None, 2100 mol\nWarning: Setting NetCDF variable compression requires compiling with HDF5 support.\nWarning: Setting NetCDF frame chunk size requires compiling with HDF5 support.\n.....................................................\nACTIVE OUTPUT TRAJECTORIES (1):\n  /tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033/output.netcdf (coordinates)\n----- cpptraj.traj.dcd (1-50, 1) -----\n 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.\n\nRead 50 frames and processed 50 frames.\nTIME: Avg. throughput= 966.5758 frames / second.\n\nACTION OUTPUT:\nTIME: Analyses took 0.0000 seconds.\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.02%)\nTIME:\t\tTrajectory Process : 0.0517 s ( 98.78%)\nTIME:\t\tAction Post        : 0.0000 s (  0.00%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0000 s (  0.00%)\nTIME:\t\tOther              : 0.0006 s (  0.01%)\nTIME:\tRun Total 0.0524 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.0861 seconds.\n--------------------------------------------------------------------------------\nTo cite CPPTRAJ use:\nDaniel R. Roe and Thomas E. Cheatham, III, &amp;quot;PTRAJ and CPPTRAJ: Software for\n  Processing and Analysis of Molecular Dynamics Trajectory Data&amp;quot;. J. Chem.\n  Theory Comput., 2013, 9 (7), pp 3084-3095.\n\n\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/cpptraj_strip/sandbox_aca3b8f4-7c87-4eba-8342-5cc381b31033&amp;#x27;, &amp;#x27;dc62adab-8b59-4ba5-b892-58d510bf15cc&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/cpptraj_strip/cpptraj_strip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_cluster.py::TestGMXCluster::test_cluster&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_cluster.py::TestGMXCluster::test_cluster&#34;, &#34;duration&#34;: &#34;00:00:53&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_cluster.py::TestGMXCluster::test_cluster&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:53&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:44:31,494 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_cluster Version: 5.0.1\n2025-01-08 09:44:31,495 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583 directory successfully created\n2025-01-08 09:44:31,498 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\n2025-01-08 09:44:31,520 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\n2025-01-08 09:44:31,521 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\n2025-01-08 09:44:31,522 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_cluster/0b82994d-ee38-4b58-9191-c335e8b45a79.stdin to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\n2025-01-08 09:44:31,523 [MainThread  ] [INFO ]  gmx cluster -g /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr -f /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/trajectory.trr -cl /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/0b82994d-ee38-4b58-9191-c335e8b45a79.stdin\n\n2025-01-08 09:44:32,969 [MainThread  ] [INFO ]  Executing: gmx cluster -g /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f...\n2025-01-08 09:44:32,969 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:44:32,970 [MainThread  ] [INFO ]  Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:44:32,970 [MainThread  ] [INFO ]                 :-) GROMACS - gmx cluster, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_cluster\nCommand line:\n  gmx cluster -g /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr -f /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/trajectory.trr -cl /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/index.ndx\n\nUsing linkage method for clustering\nReading file /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr, VERSION 2019.1 (single precision)\n\nSelect group for least squares fit and RMSD calculation:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: \nSelect group for output:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAllocated 7082160 bytes for frames\nRead 11 frames from trajectory /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/trajectory.trr\nComputing 11x11 RMS deviation matrix\n\r# RMSD calculations left: 45   \r# RMSD calculations left: 36   \r# RMSD calculations left: 28   \r# RMSD calculations left: 21   \r# RMSD calculations left: 15   \r# RMSD calculations left: 10   \r# RMSD calculations left: 6   \r# RMSD calculations left: 3   \r# RMSD calculations left: 1   \r# RMSD calculations left: 0   \r# RMSD calculations left: 0   \n\nThe RMSD ranges from 1.80823 to 3.12553 nm\nAverage RMSD is 2.45651\nNumber of structures for matrix 11\nEnergy of the matrix is 34.476.\nWARNING: rmsd cutoff 0.1 is outside range of rmsd values 1.80823 to 3.12553\nWARNING: rmsd minimum 0 is below lowest rmsd value 1.80823\nLinking structures *\nSorting and renumbering clusters\n\nFound 11 clusters\n\nWriting middle structure for each cluster to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/output_pdb.pdb\nWriting rms distance/clustering matrix   9%\b\b\b\b 18%\b\b\b\b 27%\b\b\b\b 36%\b\b\b\b 45%\b\b\b\b 54%\b\b\b\b 63%\b\b\b\b 72%\b\b\b\b 81%\b\b\b\b 90%\b\b\b\b100%\b\b\b\b\n\nGROMACS reminds you: &amp;quot;You Fill Me With Inertia&amp;quot; (The Long Blondes)\n\n\n2025-01-08 09:44:33,025 [MainThread  ] [INFO ]  Removed: [&amp;#x27;gmx_cluster_rmsd-dist.xvg&amp;#x27;, &amp;#x27;gmx_cluster_rmsd-clust.xpm&amp;#x27;, &amp;#x27;gmx_cluster_cluster.log&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_cluster/0b82994d-ee38-4b58-9191-c335e8b45a79.stdin&amp;#x27;]\n2025-01-08 09:44:33,026 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_cluster/output_pdb.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_2/gmx_cluster/output_pdb.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_cluster.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 1.0576475640718142e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_cluster Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583 directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_cluster/0b82994d-ee38-4b58-9191-c335e8b45a79.stdin to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:63 gmx cluster -g /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr -f /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/trajectory.trr -cl /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/0b82994d-ee38-4b58-9191-c335e8b45a79.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:36 Executing: gmx cluster -g /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f...\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:cmd_wrapper.py:41 Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx cluster, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_cluster\nCommand line:\n  gmx cluster -g /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_cluster.log -dist /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-dist.xvg -o /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/gmx_cluster_rmsd-clust.xpm -s /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr -f /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/trajectory.trr -cl /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/output_pdb.pdb -cutoff 0.1 -method linkage -n /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/index.ndx\n\nUsing linkage method for clustering\nReading file /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/topology.tpr, VERSION 2019.1 (single precision)\n\nSelect group for least squares fit and RMSD calculation:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: \nSelect group for output:\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAllocated 7082160 bytes for frames\nRead 11 frames from trajectory /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/trajectory.trr\nComputing 11x11 RMS deviation matrix\n\r# RMSD calculations left: 45   \r# RMSD calculations left: 36   \r# RMSD calculations left: 28   \r# RMSD calculations left: 21   \r# RMSD calculations left: 15   \r# RMSD calculations left: 10   \r# RMSD calculations left: 6   \r# RMSD calculations left: 3   \r# RMSD calculations left: 1   \r# RMSD calculations left: 0   \r# RMSD calculations left: 0   \n\nThe RMSD ranges from 1.80823 to 3.12553 nm\nAverage RMSD is 2.45651\nNumber of structures for matrix 11\nEnergy of the matrix is 34.476.\nWARNING: rmsd cutoff 0.1 is outside range of rmsd values 1.80823 to 3.12553\nWARNING: rmsd minimum 0 is below lowest rmsd value 1.80823\nLinking structures *\nSorting and renumbering clusters\n\nFound 11 clusters\n\nWriting middle structure for each cluster to /tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583/output_pdb.pdb\nWriting rms distance/clustering matrix   9%\b\b\b\b 18%\b\b\b\b 27%\b\b\b\b 36%\b\b\b\b 45%\b\b\b\b 54%\b\b\b\b 63%\b\b\b\b 72%\b\b\b\b 81%\b\b\b\b 90%\b\b\b\b100%\b\b\b\b\n\nGROMACS reminds you: &amp;quot;You Fill Me With Inertia&amp;quot; (The Long Blondes)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409 Removed: [&amp;#x27;gmx_cluster_rmsd-dist.xvg&amp;#x27;, &amp;#x27;gmx_cluster_rmsd-clust.xpm&amp;#x27;, &amp;#x27;gmx_cluster_cluster.log&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_cluster/sandbox_a41d329e-f338-4a6d-9d4f-2d185b192583&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_cluster/0b82994d-ee38-4b58-9191-c335e8b45a79.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_cluster/gmx_cluster_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_energy.py::TestGMXEnergy::test_energy&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_energy.py::TestGMXEnergy::test_energy&#34;, &#34;duration&#34;: &#34;502 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_energy.py::TestGMXEnergy::test_energy&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;502 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:45:24,437 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_energy Version: 5.0.1\n2025-01-08 09:45:24,438 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3 directory successfully created\n2025-01-08 09:45:24,439 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/energy.edr to /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3\n2025-01-08 09:45:24,439 [MainThread  ] [INFO ]  gmx energy -f /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/energy.edr -o /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/output.xvg -xvg none &amp;lt; b556aea9-262c-4a59-8436-fa467bc37625/instructions.in\n\n2025-01-08 09:45:24,488 [MainThread  ] [INFO ]  Executing: gmx energy -f /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8...\n2025-01-08 09:45:24,489 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:45:24,490 [MainThread  ] [INFO ]  \nStatistics over 501 steps [ 0.0000 through 1.0000 ps ], 2 data sets\nAll statistics are over 51 points\n\nEnergy                      Average   Err.Est.       RMSD  Tot-Drift\n-------------------------------------------------------------------------------\nPotential                -2.39705e+06         --    1223.89    6280.48  (kJ/mol)\nPressure                   0.342962         --    73.8495    27.2604  (bar)\n\n2025-01-08 09:45:24,490 [MainThread  ] [INFO ]                  :-) GROMACS - gmx energy, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_energy\nCommand line:\n  gmx energy -f /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/energy.edr -o /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/output.xvg -xvg none\n\nOpened /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/energy.edr as single precision energy file\n\nSelect the terms you want from the following list by\nselecting either (part of) the name or the number or a combination.\nEnd your selection with an empty line or a zero.\n-------------------------------------------------------------------\n  1  Angle            2  Proper-Dih.      3  Improper-Dih.    4  LJ-14         \n  5  Coulomb-14       6  LJ-(SR)          7  Coulomb-(SR)     8  Coul.-recip.  \n  9  Position-Rest.  10  Potential       11  Kinetic-En.     12  Total-Energy  \n 13  Temperature     14  Pressure        15  Constr.-rmsd    16  Box-X         \n 17  Box-Y           18  Box-Z           19  Volume          20  Density       \n 21  pV              22  Enthalpy        23  Vir-XX          24  Vir-XY        \n 25  Vir-XZ          26  Vir-YX          27  Vir-YY          28  Vir-YZ        \n 29  Vir-ZX          30  Vir-ZY          31  Vir-ZZ          32  Pres-XX       \n 33  Pres-XY         34  Pres-XZ         35  Pres-YX         36  Pres-YY       \n 37  Pres-YZ         38  Pres-ZX         39  Pres-ZY         40  Pres-ZZ       \n 41  #Surf*SurfTen   42  Box-Vel-XX      43  Box-Vel-YY      44  Box-Vel-ZZ    \n 45  Mu-X            46  Mu-Y            47  Mu-Z            48  T-Protein     \n 49  T-non-Protein                       50  Lamb-Protein                      \n 51  Lamb-non-Protein                  \n\n\rReading energy frame      0 time    0.000         \rReading energy frame      1 time    1.000         \rLast energy frame read 1 time    1.000         \n\nGROMACS reminds you: &amp;quot;Louis Pasteur&amp;#x27;s theory of germs is ridiculous fiction.&amp;quot; (Pierre Pachet, Professor of Physiology at Toulouse, 1872)\n\n\n2025-01-08 09:45:24,492 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3&amp;#x27;, &amp;#x27;b556aea9-262c-4a59-8436-fa467bc37625&amp;#x27;]\n2025-01-08 09:45:24,493 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_energy/output.xvg\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/gmx_energy/output.xvg\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_energy.xvg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_energy Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3 directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/energy.edr to /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:63 gmx energy -f /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/energy.edr -o /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/output.xvg -xvg none &amp;lt; b556aea9-262c-4a59-8436-fa467bc37625/instructions.in\n\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:36 Executing: gmx energy -f /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8...\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:cmd_wrapper.py:41 \nStatistics over 501 steps [ 0.0000 through 1.0000 ps ], 2 data sets\nAll statistics are over 51 points\n\nEnergy                      Average   Err.Est.       RMSD  Tot-Drift\n-------------------------------------------------------------------------------\nPotential                -2.39705e+06         --    1223.89    6280.48  (kJ/mol)\nPressure                   0.342962         --    73.8495    27.2604  (bar)\n\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.err:cmd_wrapper.py:49                 :-) GROMACS - gmx energy, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_energy\nCommand line:\n  gmx energy -f /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/energy.edr -o /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/output.xvg -xvg none\n\nOpened /tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3/energy.edr as single precision energy file\n\nSelect the terms you want from the following list by\nselecting either (part of) the name or the number or a combination.\nEnd your selection with an empty line or a zero.\n-------------------------------------------------------------------\n  1  Angle            2  Proper-Dih.      3  Improper-Dih.    4  LJ-14         \n  5  Coulomb-14       6  LJ-(SR)          7  Coulomb-(SR)     8  Coul.-recip.  \n  9  Position-Rest.  10  Potential       11  Kinetic-En.     12  Total-Energy  \n 13  Temperature     14  Pressure        15  Constr.-rmsd    16  Box-X         \n 17  Box-Y           18  Box-Z           19  Volume          20  Density       \n 21  pV              22  Enthalpy        23  Vir-XX          24  Vir-XY        \n 25  Vir-XZ          26  Vir-YX          27  Vir-YY          28  Vir-YZ        \n 29  Vir-ZX          30  Vir-ZY          31  Vir-ZZ          32  Pres-XX       \n 33  Pres-XY         34  Pres-XZ         35  Pres-YX         36  Pres-YY       \n 37  Pres-YZ         38  Pres-ZX         39  Pres-ZY         40  Pres-ZZ       \n 41  #Surf*SurfTen   42  Box-Vel-XX      43  Box-Vel-YY      44  Box-Vel-ZZ    \n 45  Mu-X            46  Mu-Y            47  Mu-Z            48  T-Protein     \n 49  T-non-Protein                       50  Lamb-Protein                      \n 51  Lamb-non-Protein                  \n\n\rReading energy frame      0 time    0.000         \rReading energy frame      1 time    1.000         \rLast energy frame read 1 time    1.000         \n\nGROMACS reminds you: &amp;quot;Louis Pasteur&amp;#x27;s theory of germs is ridiculous fiction.&amp;quot; (Pierre Pachet, Professor of Physiology at Toulouse, 1872)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_energy/sandbox_df04e4ac-196e-404d-a493-8eba284eaaa3&amp;#x27;, &amp;#x27;b556aea9-262c-4a59-8436-fa467bc37625&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_energy/gmx_energy_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_image.py::TestGMXImage::test_image&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_image.py::TestGMXImage::test_image&#34;, &#34;duration&#34;: &#34;756 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_image.py::TestGMXImage::test_image&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;756 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:45:24,985 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_image Version: 5.0.1\n2025-01-08 09:45:24,986 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf directory successfully created\n2025-01-08 09:45:25,000 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\n2025-01-08 09:45:25,003 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\n2025-01-08 09:45:25,004 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\n2025-01-08 09:45:25,005 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_image/60fb017c-8160-4b02-847a-e50d25579050.stdin to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\n2025-01-08 09:45:25,006 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/trajectory.trr -s /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/output.xtc -n /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/index.ndx -center &amp;lt; /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/60fb017c-8160-4b02-847a-e50d25579050.stdin\n\n2025-01-08 09:45:25,248 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f...\n2025-01-08 09:45:25,249 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:45:25,249 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for least squares fit\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for centering\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:45:25,250 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_image\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/trajectory.trr -s /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/output.xtc -n /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/index.ndx -center\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nReading file /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;The sign of wisdom is to have more questions than answers.&amp;quot; (Abhijit Naskar)\n\n\n2025-01-08 09:45:25,256 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_image/60fb017c-8160-4b02-847a-e50d25579050.stdin&amp;#x27;]\n2025-01-08 09:45:25,257 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_image/output.xtc\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/gmx_image/output.xtc\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_image.xtc\n     SIZE_A: 1167844 bytes\n     SIZE_B: 1167844 bytes\n     TOLERANCE: 1.0%, Low: 1156165.56 bytes, High: 1179522.44 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_image Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_image/60fb017c-8160-4b02-847a-e50d25579050.stdin to /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/trajectory.trr -s /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/output.xtc -n /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/index.ndx -center &amp;lt; /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/60fb017c-8160-4b02-847a-e50d25579050.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f...\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for least squares fit\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for centering\nSelected 0: &amp;#x27;System&amp;#x27;\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_image\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/trajectory.trr -s /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr -fit rot+trans -o /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/output.xtc -n /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/index.ndx -center\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nReading file /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Group     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;The sign of wisdom is to have more questions than answers.&amp;quot; (Abhijit Naskar)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_image/sandbox_9e0d3ec6-4b23-4616-902a-f53b9f1093bf&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_image/60fb017c-8160-4b02-847a-e50d25579050.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_image/gmx_image_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rgyr.py::TestGMXRgyr::test_rgyr&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rgyr.py::TestGMXRgyr::test_rgyr&#34;, &#34;duration&#34;: &#34;686 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_rgyr.py::TestGMXRgyr::test_rgyr&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;686 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:45:25,725 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_rgyr Version: 5.0.1\n2025-01-08 09:45:25,726 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55 directory successfully created\n2025-01-08 09:45:25,729 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\n2025-01-08 09:45:25,741 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\n2025-01-08 09:45:25,742 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\n2025-01-08 09:45:25,743 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_rgyr/dcbe055a-514f-48c6-a127-a047c522384a.stdin to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\n2025-01-08 09:45:25,743 [MainThread  ] [INFO ]  gmx gyrate -s /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr -f /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/dcbe055a-514f-48c6-a127-a047c522384a.stdin\n\n2025-01-08 09:45:25,940 [MainThread  ] [INFO ]  Executing: gmx gyrate -s /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff8...\n2025-01-08 09:45:25,941 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:45:25,941 [MainThread  ] [INFO ]                  :-) GROMACS - gmx gyrate, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_rgyr\nCommand line:\n  gmx gyrate -s /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr -f /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/index.ndx\n\nReading file /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr, VERSION 2019.1 (single precision)\ntrr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAnalyzed 11 frames, last time 100.000\n\nGROMACS reminds you: &amp;quot;The sign of wisdom is to have more questions than answers.&amp;quot; (Abhijit Naskar)\n\n\n2025-01-08 09:45:25,945 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_rgyr/dcbe055a-514f-48c6-a127-a047c522384a.stdin&amp;#x27;]\n2025-01-08 09:45:25,946 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_rgyr/output.xvg\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/gmx_rgyr/output.xvg\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_rgyr.xvg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_rgyr Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55 directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_rgyr/dcbe055a-514f-48c6-a127-a047c522384a.stdin to /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:cmd_wrapper.py:63 gmx gyrate -s /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr -f /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/dcbe055a-514f-48c6-a127-a047c522384a.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:cmd_wrapper.py:36 Executing: gmx gyrate -s /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff8...\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.err:cmd_wrapper.py:49                 :-) GROMACS - gmx gyrate, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_rgyr\nCommand line:\n  gmx gyrate -s /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr -f /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/index.ndx\n\nReading file /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55/topology.tpr, VERSION 2019.1 (single precision)\ntrr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \nAnalyzed 11 frames, last time 100.000\n\nGROMACS reminds you: &amp;quot;The sign of wisdom is to have more questions than answers.&amp;quot; (Abhijit Naskar)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_rgyr/sandbox_46dc7cc5-7853-4d82-8f44-ff866de62c55&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_rgyr/dcbe055a-514f-48c6-a127-a047c522384a.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_rgyr/gmx_rgyr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rms.py::TestGMXRms::test_rms&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_rms.py::TestGMXRms::test_rms&#34;, &#34;duration&#34;: &#34;694 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_rms.py::TestGMXRms::test_rms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;694 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:45:26,420 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_rms Version: 5.0.1\n2025-01-08 09:45:26,421 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210 directory successfully created\n2025-01-08 09:45:26,423 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\n2025-01-08 09:45:26,436 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\n2025-01-08 09:45:26,437 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\n2025-01-08 09:45:26,438 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_rms/d7f490e5-2001-42db-92a5-03c26ba4cd49.stdin to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\n2025-01-08 09:45:26,438 [MainThread  ] [INFO ]  gmx rms -s /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr -f /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/d7f490e5-2001-42db-92a5-03c26ba4cd49.stdin\n\n2025-01-08 09:45:26,641 [MainThread  ] [INFO ]  Executing: gmx rms -s /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba...\n2025-01-08 09:45:26,642 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:45:26,642 [MainThread  ] [INFO ]  Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:45:26,643 [MainThread  ] [INFO ]                   :-) GROMACS - gmx rms, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_rms\nCommand line:\n  gmx rms -s /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr -f /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/index.ndx\n\nReading file /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr, VERSION 2019.1 (single precision)\nSelect group for least squares fit\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Select group for RMSD calculation\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \n\nGROMACS reminds you: &amp;quot;Your theory is crazy, but it&amp;#x27;s not crazy enough to be true.&amp;quot; (Niels Bohr)\n\n\n2025-01-08 09:45:26,647 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_rms/d7f490e5-2001-42db-92a5-03c26ba4cd49.stdin&amp;#x27;]\n2025-01-08 09:45:26,648 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_rms/output.xvg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_rms Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210 directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_rms/d7f490e5-2001-42db-92a5-03c26ba4cd49.stdin to /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:63 gmx rms -s /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr -f /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/d7f490e5-2001-42db-92a5-03c26ba4cd49.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:36 Executing: gmx rms -s /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba...\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:cmd_wrapper.py:41 Selected 0: &amp;#x27;System&amp;#x27;\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.err:cmd_wrapper.py:49                  :-) GROMACS - gmx rms, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_rms\nCommand line:\n  gmx rms -s /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr -f /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/trajectory.trr -o /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/output.xvg -xvg none -n /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/index.ndx\n\nReading file /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210/topology.tpr, VERSION 2019.1 (single precision)\nSelect group for least squares fit\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: Select group for RMSD calculation\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       2 time   20.000   \rReading frame       3 time   30.000   \rReading frame       4 time   40.000   \rReading frame       5 time   50.000   \rReading frame       6 time   60.000   \rReading frame       7 time   70.000   \rReading frame       8 time   80.000   \rReading frame       9 time   90.000   \rReading frame      10 time  100.000   \rLast frame         10 time  100.000   \n\nGROMACS reminds you: &amp;quot;Your theory is crazy, but it&amp;#x27;s not crazy enough to be true.&amp;quot; (Niels Bohr)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_rms/sandbox_662000f8-39a7-489e-8cf2-eb0a4ba93210&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_rms/d7f490e5-2001-42db-92a5-03c26ba4cd49.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_rms/gmx_rms_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str.py::TestGMXTrjConvStr::test_trjconv_str&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str.py::TestGMXTrjConvStr::test_trjconv_str&#34;, &#34;duration&#34;: &#34;00:00:47&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str.py::TestGMXTrjConvStr::test_trjconv_str&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:47&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:45:27,121 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_trjconv_str Version: 5.0.1\n2025-01-08 09:45:27,122 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e directory successfully created\n2025-01-08 09:45:27,135 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\n2025-01-08 09:45:27,138 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\n2025-01-08 09:45:27,139 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\n2025-01-08 09:45:27,140 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_trjconv_str/9a0e1771-3032-44e9-8803-3411d9fc806f.stdin to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\n2025-01-08 09:45:27,140 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr -o /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/output.pdb -nocenter -n /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/9a0e1771-3032-44e9-8803-3411d9fc806f.stdin\n\n2025-01-08 09:45:28,358 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-...\n2025-01-08 09:45:28,359 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:45:28,359 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:45:28,360 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_trjconv_str\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr -o /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/output.pdb -nocenter -n /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.&amp;quot; (Max Planck)\n\n\n2025-01-08 09:45:28,421 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str/9a0e1771-3032-44e9-8803-3411d9fc806f.stdin&amp;#x27;]\n2025-01-08 09:45:28,422 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_trjconv_str/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_2/gmx_trjconv_str/output.pdb\n     PDB_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_trjconv.str.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 1.329478924728574e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_trjconv_str Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_trjconv_str/9a0e1771-3032-44e9-8803-3411d9fc806f.stdin to /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr -o /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/output.pdb -nocenter -n /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/9a0e1771-3032-44e9-8803-3411d9fc806f.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-...\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_trjconv_str\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr -o /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/output.pdb -nocenter -n /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rReading frame       2 time   20.000    -&amp;gt;  frame      1 time   10.000      \r\rReading frame       3 time   30.000    -&amp;gt;  frame      2 time   20.000      \r\rReading frame       4 time   40.000    -&amp;gt;  frame      3 time   30.000      \r\rReading frame       5 time   50.000    -&amp;gt;  frame      4 time   40.000      \r\rReading frame       6 time   60.000    -&amp;gt;  frame      5 time   50.000      \r\rReading frame       7 time   70.000    -&amp;gt;  frame      6 time   60.000      \r\rReading frame       8 time   80.000    -&amp;gt;  frame      7 time   70.000      \r\rReading frame       9 time   90.000    -&amp;gt;  frame      8 time   80.000      \r\rReading frame      10 time  100.000    -&amp;gt;  frame      9 time   90.000      \r\rLast frame         10 time  100.000   \n -&amp;gt;  frame     10 time  100.000      \r\nLast written: frame     10 time  100.000\n\n\nGROMACS reminds you: &amp;quot;A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.&amp;quot; (Max Planck)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str/sandbox_a409a734-cf23-4532-9895-a6972db0941e&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str/9a0e1771-3032-44e9-8803-3411d9fc806f.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str/gmx_trjconv_str_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str_ens.py::TestGMXTrjConvStrEns::test_trjconv_str_ens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str_ens.py::TestGMXTrjConvStrEns::test_trjconv_str_ens&#34;, &#34;duration&#34;: &#34;00:00:13&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_str_ens.py::TestGMXTrjConvStrEns::test_trjconv_str_ens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:13&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:46:14,237 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_trjconv_str_ens Version: 5.0.1\n2025-01-08 09:46:14,238 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c directory successfully created\n2025-01-08 09:46:14,253 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\n2025-01-08 09:46:14,255 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\n2025-01-08 09:46:14,256 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\n2025-01-08 09:46:14,257 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_trjconv_str_ens/4f1c26a5-c06d-4aea-af82-a0aaf855397f.stdin to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\n2025-01-08 09:46:14,258 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output.pdb -e 10 -n /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/4f1c26a5-c06d-4aea-af82-a0aaf855397f.stdin\n\n2025-01-08 09:46:14,557 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-4...\n2025-01-08 09:46:14,558 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:46:14,558 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:46:14,559 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_trjconv_str_ens\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output.pdb -e 10 -n /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rLast frame          1 time   10.000   \n -&amp;gt;  frame      1 time   10.000      \r\nLast written: frame      1 time   10.000\n\n\nGROMACS reminds you: &amp;quot;You Can Always Go On Ricky Lake&amp;quot; (Offspring)\n\n\n2025-01-08 09:46:14,594 [MainThread  ] [INFO ]  Adding:\n2025-01-08 09:46:14,595 [MainThread  ] [INFO ]  [PosixPath(&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output0.pdb&amp;#x27;), PosixPath(&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output1.pdb&amp;#x27;)]\n2025-01-08 09:46:14,595 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output.zip\n2025-01-08 09:46:14,608 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/4f1c26a5-c06d-4aea-af82-a0aaf855397f.stdin&amp;#x27;]\n2025-01-08 09:46:14,609 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_trjconv_str_ens/output.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_2/gmx_trjconv_str_ens/output.zip\nCreating a unique_dir for: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_trjconv.str.ens.zip\nChecking RMSD between:\n     PDB_A: 67c4f38c-a038-42a7-ae23-cbdc48a3893b/output0.pdb\n     PDB_B: 89b4005f-7d42-460c-8ba1-fec6fdf858c1/output0.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 1.329478924728574e-14\n     RMS_CUTOFF: 1\nChecking RMSD between:\n     PDB_A: 67c4f38c-a038-42a7-ae23-cbdc48a3893b/output1.pdb\n     PDB_B: 89b4005f-7d42-460c-8ba1-fec6fdf858c1/output1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 10095\n     Atoms ALIGNED in PDB_B: 10095\n     RMS: 6.247194817921177e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_trjconv_str_ens Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/topology.tpr to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_trjconv_str_ens/4f1c26a5-c06d-4aea-af82-a0aaf855397f.stdin to /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output.pdb -e 10 -n /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/4f1c26a5-c06d-4aea-af82-a0aaf855397f.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-4...\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_trjconv_str_ens\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/trajectory.trr -s /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr -skip 1 -b 0 -dt 1 -sep -o /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output.pdb -e 10 -n /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/index.ndx\n\nWill write pdb: Protein data bank file\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr, VERSION 2019.1 (single precision)\nReading file /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/topology.tpr, VERSION 2019.1 (single precision)\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000    -&amp;gt;  frame      0 time    0.000      \r\rLast frame          1 time   10.000   \n -&amp;gt;  frame      1 time   10.000      \r\nLast written: frame      1 time   10.000\n\n\nGROMACS reminds you: &amp;quot;You Can Always Go On Ricky Lake&amp;quot; (Offspring)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:149 [PosixPath(&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output0.pdb&amp;#x27;), PosixPath(&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output1.pdb&amp;#x27;)]\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:150 to: /tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c/output.zip\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/sandbox_d67acfc0-a152-40e8-82b8-baabc09ba04c&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_str_ens/4f1c26a5-c06d-4aea-af82-a0aaf855397f.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_str_ens/gmx_trjconv_str_ens_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}], &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_trj.py::TestGMXTrjConvTrj::test_trjconv_trj&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_trj.py::TestGMXTrjConvTrj::test_trjconv_trj&#34;, &#34;duration&#34;: &#34;522 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_analysis/test/unitests/test_gromacs/test_gmx_trjconv_trj.py::TestGMXTrjConvTrj::test_trjconv_trj&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;522 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2025-01-08 09:46:26,785 [MainThread  ] [INFO ]  Module: biobb_analysis.gromacs.gmx_trjconv_trj Version: 5.0.1\n2025-01-08 09:46:26,786 [MainThread  ] [INFO ]  /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d directory successfully created\n2025-01-08 09:46:26,800 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d\n2025-01-08 09:46:26,801 [MainThread  ] [INFO ]  Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d\n2025-01-08 09:46:26,802 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_2/gmx_trjconv_trj/94437ad1-a3c4-496f-be9c-e65260c06338.stdin to /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d\n2025-01-08 09:46:26,802 [MainThread  ] [INFO ]  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/output.xtc -n /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/94437ad1-a3c4-496f-be9c-e65260c06338.stdin\n\n2025-01-08 09:46:26,859 [MainThread  ] [INFO ]  Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-...\n2025-01-08 09:46:26,860 [MainThread  ] [INFO ]  Exit code: 0\n2025-01-08 09:46:26,860 [MainThread  ] [INFO ]  Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\n2025-01-08 09:46:26,860 [MainThread  ] [INFO ]                 :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_trjconv_trj\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/output.xtc -n /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/index.ndx\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rLast frame          0 time    0.000   \n -&amp;gt;  frame      0 time    0.000      \r\nLast written: frame      0 time    0.000\n\n\nGROMACS reminds you: &amp;quot;Microsecond Here I Come&amp;quot; (P.J. Van Maaren)\n\n\n2025-01-08 09:46:26,864 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_trj/94437ad1-a3c4-496f-be9c-e65260c06338.stdin&amp;#x27;]\n2025-01-08 09:46:26,865 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_2/gmx_trjconv_trj/output.xtc\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_2/gmx_trjconv_trj/output.xtc\n     FILE_B: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/reference/gromacs/ref_trjconv.trj.xtc\n     SIZE_A: 108280 bytes\n     SIZE_B: 108280 bytes\n     TOLERANCE: 1.0%, Low: 107197.2 bytes, High: 109362.8 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Module: biobb_analysis.gromacs.gmx_trjconv_trj Version: 5.0.1\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:82 /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d directory successfully created\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/trajectory.trr to /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Copy: /home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis/biobb_analysis/test/data/gromacs/index.ndx to /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Copy: /tmp/biobb/unitests_2/gmx_trjconv_trj/94437ad1-a3c4-496f-be9c-e65260c06338.stdin to /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:63 gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/output.xtc -n /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/index.ndx &amp;lt; /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/94437ad1-a3c4-496f-be9c-e65260c06338.stdin\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:36 Executing: gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-...\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:cmd_wrapper.py:41 Note that major changes are planned in future for trjconv, to improve usability and utility.\nSelect group for output\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.err:cmd_wrapper.py:49                :-) GROMACS - gmx trjconv, 2024.4-conda_forge (-:\n\nExecutable:   /home/gbayarri/micromamba/envs/test_environment/bin.SSE2/gmx\nData prefix:  /home/gbayarri/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_2/gmx_trjconv_trj\nCommand line:\n  gmx trjconv -f /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/trajectory.trr -b 0 -e 0 -dt 0 -o /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/output.xtc -n /tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d/index.ndx\n\nWill write xtc: Compressed trajectory (portable xdr format): xtc\nGroup     0 (         System) has 29509 elements\nGroup     1 (            DNA) has   758 elements\nSelect a group: trr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \nSetting output precision to 0.001 (nm)\n\rLast frame          0 time    0.000   \n -&amp;gt;  frame      0 time    0.000      \r\nLast written: frame      0 time    0.000\n\n\nGROMACS reminds you: &amp;quot;Microsecond Here I Come&amp;quot; (P.J. Van Maaren)\n\n\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_trj/sandbox_892c3494-89ca-4373-8200-737c27fad13d&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_2/gmx_trjconv_trj/94437ad1-a3c4-496f-be9c-e65260c06338.stdin&amp;#x27;]\nINFO     /tmp/biobb/unitests_2/gmx_trjconv_trj/gmx_trjconv_trj_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_2\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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