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-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.16&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityDefault::test_cpptraj_density&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityDefault::test_cpptraj_density&#34;, &#34;duration&#34;: &#34;193 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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityDefault::test_cpptraj_density&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;193 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 -----------------------------\n\ncmd_wrapper commnand print: cpptraj -i 2da0f2eb-291a-4503-9631-b5e9ebb02053/instructions.in\nExecuting: cpptraj -i 2da0f2eb-291a-4503-9631-b5e9ebb02053/instructions.in...\nExit code: 0\n\nChecking if empty file: /tmp/biobb/unitests_106/cpptraj_density/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_106/cpptraj_density/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/ambertools/density_default.dat\n        File_A hash: b&amp;#x27;\\xe14\\x16\\xd5\\xbf\\xdc\\xd7\\x83\\x07\\x1c\\x9e\\xf3\\xf4\\x80\\x84\\xdd\\xe1=VBv\\xb5\\x8e\\tu\\xaa\\xf4\\x9dfR^\\xab&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe14\\x16\\xd5\\xbf\\xdc\\xd7\\x83\\x07\\x1c\\x9e\\xf3\\xf4\\x80\\x84\\xdd\\xe1=VBv\\xb5\\x8e\\tu\\xaa\\xf4\\x9dfR^\\xab&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityMask::test_cpptraj_density&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityMask::test_cpptraj_density&#34;, &#34;duration&#34;: &#34;176 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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityMask::test_cpptraj_density&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;176 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 -----------------------------\n\ncmd_wrapper commnand print: cpptraj -i 137c7640-72f7-40f9-8ad2-d2a416102d50/instructions.in\nExecuting: cpptraj -i 137c7640-72f7-40f9-8ad2-d2a416102d50/instructions.in...\nExit code: 0\n\nChecking if empty file: /tmp/biobb/unitests_106/cpptraj_density_mask/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_106/cpptraj_density_mask/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/ambertools/density_mask.dat\n        File_A hash: b&amp;quot;\\xd6\\xf4\\x07\\x8c:\\xb0\\xe5&amp;#x27;~\\x92\\\\\\xb4\\x11N\\xbf\\xbe\\x93\\xe7~\\xba\\xcf\\xd1JX\\x8a~\\xcb&amp;amp;ay\\x94\\xf7&amp;quot;\n        File_B hash: b&amp;quot;\\xd6\\xf4\\x07\\x8c:\\xb0\\xe5&amp;#x27;~\\x92\\\\\\xb4\\x11N\\xbf\\xbe\\x93\\xe7~\\xba\\xcf\\xd1JX\\x8a~\\xcb&amp;amp;ay\\x94\\xf7&amp;quot;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityComplex::test_cpptraj_density&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityComplex::test_cpptraj_density&#34;, &#34;duration&#34;: &#34;177 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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityComplex::test_cpptraj_density&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;177 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 -----------------------------\n2024-12-16 12:05:12,446 [MainThread  ] [INFO ]  Module: biobb_mem.ambertools.cpptraj_density Version: 5.0.4\n2024-12-16 12:05:12,447 [MainThread  ] [INFO ]  /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4 directory successfully created\n2024-12-16 12:05:12,450 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/topology.pdb to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4\n2024-12-16 12:05:12,452 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/trajectory.xtc to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4\n2024-12-16 12:05:12,453 [MainThread  ] [INFO ]  cpptraj -i 3e56c7ed-eb54-4b26-9373-d456008d6ef5/instructions.in\n\n2024-12-16 12:05:12,599 [MainThread  ] [INFO ]  Executing: cpptraj -i 3e56c7ed-eb54-4b26-9373-d456008d6ef5/instructions.in...\n2024-12-16 12:05:12,599 [MainThread  ] [INFO ]  Exit code: 0\n2024-12-16 12:05:12,599 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 12/16/24 12:05:12\n| Available memory: 6.270 GB\n\nINPUT: Reading input from &amp;#x27;3e56c7ed-eb54-4b26-9373-d456008d6ef5/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/topology.pdb]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/topology.pdb&amp;#x27; as PDB File\n\tReading 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;topology.pdb&amp;#x27;.\n  [trajin /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/trajectory.xtc 5 15 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/trajectory.xtc&amp;#x27; as Gromacs XTC\nWarning: Box X vector length is zero.\nWarning: Box Y vector length is zero.\nWarning: Box Z vector length is zero.\nWarning: stop 15 &amp;gt; #Frames (12), setting to max.\n  [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n    DENSITY: Determining mass density for 2 masks.\n\troutine version: 1.0.3\n\tDelta is 0.140000\n\tAxis is Y\n\tData set name is &amp;#x27;DENSITY_00001&amp;#x27;\n\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n\tBin coordinates will be to bin center.\n\tOutput to &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/output.dat&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: topology.pdb, 47441 atoms, 2259 res, box: None, 599 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;trajectory.xtc&amp;#x27; is a GROMACS XTC file, Parm topology.pdb (reading 8 of 12)\n  Coordinate processing will occur on 8 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;topology.pdb&amp;#x27; (1 actions):\n  0: [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n\t [::M,A,B](36840)\n\t [::A,B](7140)\n----- trajectory.xtc (5-12, 1) -----\n 0% 14% 29% 43% 57% 71% 86% 100% Complete.\n\nRead 8 frames and processed 8 frames.\nTIME: Avg. throughput= 172.4770 frames / second.\n\nACTION OUTPUT:\n    DENSITY: The average box area in X/Z is 0.00 Angstrom (sd = 0.00).\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (4 total):\n\tDENSITY_00001[avg]:1 &amp;quot;::M,A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:1 &amp;quot;sd(::M,A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[avg]:2 &amp;quot;::A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:2 &amp;quot;sd(::A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n    Total data set memory usage is at least 41.024 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  ::M,A,B sd(::M,A,B) ::A,B sd(::A,B)\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.01%)\nTIME:\t\tTrajectory Process : 0.0464 s ( 93.24%)\nTIME:\t\tAction Post        : 0.0001 s (  0.12%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0032 s (  6.40%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0497 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1267 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\n2024-12-16 12:05:12,601 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4&amp;#x27;, &amp;#x27;3e56c7ed-eb54-4b26-9373-d456008d6ef5&amp;#x27;]\n2024-12-16 12:05:12,601 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_106/cpptraj_density_complex/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_106/cpptraj_density_complex/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/ambertools/density_complex.dat\n        File_A hash: b&amp;#x27;\\xea\\xdaj\\xb2\\x83\\x9f\\x7f\\xc1#JlL\\x88\\x00\\x82\\x18\\xda\\xfd\\x98\\xc0R\\xfe\\x10K\\xdf&amp;gt;\\xdf\\xd3\\x1bh\\x87d&amp;#x27;\n        File_B hash: b&amp;#x27;\\xea\\xdaj\\xb2\\x83\\x9f\\x7f\\xc1#JlL\\x88\\x00\\x82\\x18\\xda\\xfd\\x98\\xc0R\\xfe\\x10K\\xdf&amp;gt;\\xdf\\xd3\\x1bh\\x87d&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Module: biobb_mem.ambertools.cpptraj_density Version: 5.0.4\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:82 /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4 directory successfully created\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/topology.pdb to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/trajectory.xtc to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:63 cpptraj -i 3e56c7ed-eb54-4b26-9373-d456008d6ef5/instructions.in\n\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 3e56c7ed-eb54-4b26-9373-d456008d6ef5/instructions.in...\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 12/16/24 12:05:12\n| Available memory: 6.270 GB\n\nINPUT: Reading input from &amp;#x27;3e56c7ed-eb54-4b26-9373-d456008d6ef5/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/topology.pdb]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/topology.pdb&amp;#x27; as PDB File\n\tReading 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;topology.pdb&amp;#x27;.\n  [trajin /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/trajectory.xtc 5 15 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/trajectory.xtc&amp;#x27; as Gromacs XTC\nWarning: Box X vector length is zero.\nWarning: Box Y vector length is zero.\nWarning: Box Z vector length is zero.\nWarning: stop 15 &amp;gt; #Frames (12), setting to max.\n  [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n    DENSITY: Determining mass density for 2 masks.\n\troutine version: 1.0.3\n\tDelta is 0.140000\n\tAxis is Y\n\tData set name is &amp;#x27;DENSITY_00001&amp;#x27;\n\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n\tBin coordinates will be to bin center.\n\tOutput to &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/output.dat&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: topology.pdb, 47441 atoms, 2259 res, box: None, 599 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;trajectory.xtc&amp;#x27; is a GROMACS XTC file, Parm topology.pdb (reading 8 of 12)\n  Coordinate processing will occur on 8 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;topology.pdb&amp;#x27; (1 actions):\n  0: [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n\t [::M,A,B](36840)\n\t [::A,B](7140)\n----- trajectory.xtc (5-12, 1) -----\n 0% 14% 29% 43% 57% 71% 86% 100% Complete.\n\nRead 8 frames and processed 8 frames.\nTIME: Avg. throughput= 172.4770 frames / second.\n\nACTION OUTPUT:\n    DENSITY: The average box area in X/Z is 0.00 Angstrom (sd = 0.00).\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (4 total):\n\tDENSITY_00001[avg]:1 &amp;quot;::M,A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:1 &amp;quot;sd(::M,A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[avg]:2 &amp;quot;::A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:2 &amp;quot;sd(::A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n    Total data set memory usage is at least 41.024 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  ::M,A,B sd(::M,A,B) ::A,B sd(::A,B)\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.01%)\nTIME:\t\tTrajectory Process : 0.0464 s ( 93.24%)\nTIME:\t\tAction Post        : 0.0001 s (  0.12%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0032 s (  6.40%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0497 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1267 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_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_620fab3f-a14f-4d40-aafe-9da6fb33daf4&amp;#x27;, &amp;#x27;3e56c7ed-eb54-4b26-9373-d456008d6ef5&amp;#x27;]\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_fatslim/test_fatslim_membranes.py::TestFatslimMembranescDefault::test_fatslim_membranes&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_fatslim/test_fatslim_membranes.py::TestFatslimMembranescDefault::test_fatslim_membranes&#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_mem/test/unitests/test_fatslim/test_fatslim_membranes.py::TestFatslimMembranescDefault::test_fatslim_membranes&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 -----------------------------\nWarning: trajectory probably has no box variable. Setting dimensions ussing the minimum and maximum positions of the atoms.\n\ncmd_wrapper commnand print: gmx editconf -f /tmp/biobb/unitests_106/fatslim_membranes/sandbox_ccc8870e-3fde-40a5-8728-46b2ffea98a7/A01JD.pdb -o ecbdb7d5-c1c4-45b6-ad5f-2d8972d4d3be/output.gro -box 173.48001 168.94 122.75001 ; fatslim membranes -n af970723-8207-4d45-bcf6-9c68a2c1d15b/headgroups.ndx -c ecbdb7d5-c1c4-45b6-ad5f-2d8972d4d3be/output.gro --output-index 5d5171da-5ead-4b19-918b-d65b3a296aca/output.ndx --cutoff 2.2 --begin-frame -1 --end-frame -1\nExecuting: gmx editconf -f /tmp/biobb/unitests_106/fatslim_membranes/sandbox_ccc8870e-3fde-...\nExit code: 0\n\nChecking if empty file: /tmp/biobb/unitests_106/fatslim_membranes/leaflets.ndx\nComparing: \n        File_A: /tmp/biobb/unitests_106/fatslim_membranes/leaflets.ndx\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/fatslim/leaflets.ndx\n        File_A hash: 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b&amp;#x27;\\x87\\xc7\\x9c\\xcf\\xc3Y4P2\\x02\\xad:\\x06\\xc0O&amp;lt;\\xf9U/-\\x1e\\xf3\\xcf\\x7f@\\xea\\x19#\\x05\\xcc\\x05C&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_lipyphilic_biobb/test_lpp_zpositions.py::TestLipyphilicPositionsDefault::test_lipyphilic_positons_default&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_lipyphilic_biobb/test_lpp_zpositions.py::TestLipyphilicPositionsDefault::test_lipyphilic_positons_default&#34;, &#34;duration&#34;: &#34;583 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_mem/test/unitests/test_lipyphilic_biobb/test_lpp_zpositions.py::TestLipyphilicPositionsDefault::test_lipyphilic_positons_default&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;583 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 -----------------------------\nChecking if empty file: /tmp/biobb/unitests_106/lpp_zpositions/zpositions.csv\nComparing: \n        File_A: /tmp/biobb/unitests_106/lpp_zpositions/zpositions.csv\n        File_B: /tmp/biobb/unitests_106/lpp_zpositions/zpositions.csv\n        File_A hash: b&amp;#x27;&amp;lt;Gm\\x12\\x17\\xca\\x88\\xdb\\x12\\x8bH\\xb3\\x85V\\xfc\\xb6\\xd9\\x89FAm\\xb0\\xddK\\x90\\xb9\\xe3N\\xa7\\xbe@\\x8f&amp;#x27;\n        File_B hash: b&amp;#x27;&amp;lt;Gm\\x12\\x17\\xca\\x88\\xdb\\x12\\x8bH\\xb3\\x85V\\xfc\\xb6\\xd9\\x89FAm\\xb0\\xddK\\x90\\xb9\\xe3N\\xa7\\xbe@\\x8f&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_mdanalysis_biobb/test_mdanalays_biobb.py::TestMDAHole::test_mda_hole_default&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_mdanalysis_biobb/test_mdanalays_biobb.py::TestMDAHole::test_mda_hole_default&#34;, &#34;duration&#34;: &#34;00:00:09&#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_mem/test/unitests/test_mdanalysis_biobb/test_mdanalays_biobb.py::TestMDAHole::test_mda_hole_default&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_106/mda_hole/hole.vmd\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_106/mda_hole/hole.vmd\n     FILE_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/mdanalysis_biobb/hole.vmd\n     SIZE_A: 4535925 bytes\n     SIZE_B: 4548795 bytes\n     TOLERANCE: 1.0%, Low: 4496936.4 bytes, High: 4587783.6 bytes\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\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;3.11.11&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityDefault::test_cpptraj_density&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityDefault::test_cpptraj_density&#34;, &#34;duration&#34;: &#34;183 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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityDefault::test_cpptraj_density&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;183 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 -----------------------------\n\ncmd_wrapper commnand print: cpptraj -i ee756d62-cb61-4265-9735-6fd465a6f18b/instructions.in\nExecuting: cpptraj -i ee756d62-cb61-4265-9735-6fd465a6f18b/instructions.in...\nExit code: 0\n\nChecking if empty file: /tmp/biobb/unitests_106/cpptraj_density/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_106/cpptraj_density/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/ambertools/density_default.dat\n        File_A hash: b&amp;#x27;\\xe14\\x16\\xd5\\xbf\\xdc\\xd7\\x83\\x07\\x1c\\x9e\\xf3\\xf4\\x80\\x84\\xdd\\xe1=VBv\\xb5\\x8e\\tu\\xaa\\xf4\\x9dfR^\\xab&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe14\\x16\\xd5\\xbf\\xdc\\xd7\\x83\\x07\\x1c\\x9e\\xf3\\xf4\\x80\\x84\\xdd\\xe1=VBv\\xb5\\x8e\\tu\\xaa\\xf4\\x9dfR^\\xab&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityMask::test_cpptraj_density&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityMask::test_cpptraj_density&#34;, &#34;duration&#34;: &#34;172 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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityMask::test_cpptraj_density&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;172 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 -----------------------------\n\ncmd_wrapper commnand print: cpptraj -i afd4360c-ce5d-434b-ac19-d7eb8498afca/instructions.in\nExecuting: cpptraj -i afd4360c-ce5d-434b-ac19-d7eb8498afca/instructions.in...\nExit code: 0\n\nChecking if empty file: /tmp/biobb/unitests_106/cpptraj_density_mask/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_106/cpptraj_density_mask/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/ambertools/density_mask.dat\n        File_A hash: b&amp;quot;\\xd6\\xf4\\x07\\x8c:\\xb0\\xe5&amp;#x27;~\\x92\\\\\\xb4\\x11N\\xbf\\xbe\\x93\\xe7~\\xba\\xcf\\xd1JX\\x8a~\\xcb&amp;amp;ay\\x94\\xf7&amp;quot;\n        File_B hash: b&amp;quot;\\xd6\\xf4\\x07\\x8c:\\xb0\\xe5&amp;#x27;~\\x92\\\\\\xb4\\x11N\\xbf\\xbe\\x93\\xe7~\\xba\\xcf\\xd1JX\\x8a~\\xcb&amp;amp;ay\\x94\\xf7&amp;quot;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityComplex::test_cpptraj_density&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityComplex::test_cpptraj_density&#34;, &#34;duration&#34;: &#34;169 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_mem/test/unitests/test_ambertools/test_cpptraj_density.py::TestCpptrajDensityComplex::test_cpptraj_density&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;169 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 -----------------------------\n2024-12-16 12:14:49,337 [MainThread  ] [INFO ]  Module: biobb_mem.ambertools.cpptraj_density Version: 5.0.4\n2024-12-16 12:14:49,337 [MainThread  ] [INFO ]  /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556 directory successfully created\n2024-12-16 12:14:49,341 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/topology.pdb to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556\n2024-12-16 12:14:49,343 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/trajectory.xtc to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556\n2024-12-16 12:14:49,343 [MainThread  ] [INFO ]  cpptraj -i 9f7a988f-9c0d-43cc-aeae-701860fdedd9/instructions.in\n\n2024-12-16 12:14:49,484 [MainThread  ] [INFO ]  Executing: cpptraj -i 9f7a988f-9c0d-43cc-aeae-701860fdedd9/instructions.in...\n2024-12-16 12:14:49,485 [MainThread  ] [INFO ]  Exit code: 0\n2024-12-16 12:14:49,485 [MainThread  ] [INFO ]  \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 12/16/24 12:14:49\n| Available memory: 6.126 GB\n\nINPUT: Reading input from &amp;#x27;9f7a988f-9c0d-43cc-aeae-701860fdedd9/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/topology.pdb]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/topology.pdb&amp;#x27; as PDB File\n\tReading 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;topology.pdb&amp;#x27;.\n  [trajin /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/trajectory.xtc 5 15 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/trajectory.xtc&amp;#x27; as Gromacs XTC\nWarning: Box X vector length is zero.\nWarning: Box Y vector length is zero.\nWarning: Box Z vector length is zero.\nWarning: stop 15 &amp;gt; #Frames (12), setting to max.\n  [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n    DENSITY: Determining mass density for 2 masks.\n\troutine version: 1.0.3\n\tDelta is 0.140000\n\tAxis is Y\n\tData set name is &amp;#x27;DENSITY_00001&amp;#x27;\n\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n\tBin coordinates will be to bin center.\n\tOutput to &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/output.dat&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: topology.pdb, 47441 atoms, 2259 res, box: None, 599 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;trajectory.xtc&amp;#x27; is a GROMACS XTC file, Parm topology.pdb (reading 8 of 12)\n  Coordinate processing will occur on 8 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;topology.pdb&amp;#x27; (1 actions):\n  0: [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n\t [::M,A,B](36840)\n\t [::A,B](7140)\n----- trajectory.xtc (5-12, 1) -----\n 0% 14% 29% 43% 57% 71% 86% 100% Complete.\n\nRead 8 frames and processed 8 frames.\nTIME: Avg. throughput= 174.2654 frames / second.\n\nACTION OUTPUT:\n    DENSITY: The average box area in X/Z is 0.00 Angstrom (sd = 0.00).\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (4 total):\n\tDENSITY_00001[avg]:1 &amp;quot;::M,A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:1 &amp;quot;sd(::M,A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[avg]:2 &amp;quot;::A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:2 &amp;quot;sd(::A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n    Total data set memory usage is at least 41.024 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  ::M,A,B sd(::M,A,B) ::A,B sd(::A,B)\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.01%)\nTIME:\t\tTrajectory Process : 0.0459 s ( 92.49%)\nTIME:\t\tAction Post        : 0.0001 s (  0.13%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0035 s (  7.13%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0496 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1231 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\n2024-12-16 12:14:49,486 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556&amp;#x27;, &amp;#x27;9f7a988f-9c0d-43cc-aeae-701860fdedd9&amp;#x27;]\n2024-12-16 12:14:49,487 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_106/cpptraj_density_complex/output.dat\nComparing: \n        File_A: /tmp/biobb/unitests_106/cpptraj_density_complex/output.dat\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/ambertools/density_complex.dat\n        File_A hash: b&amp;#x27;\\xea\\xdaj\\xb2\\x83\\x9f\\x7f\\xc1#JlL\\x88\\x00\\x82\\x18\\xda\\xfd\\x98\\xc0R\\xfe\\x10K\\xdf&amp;gt;\\xdf\\xd3\\x1bh\\x87d&amp;#x27;\n        File_B hash: b&amp;#x27;\\xea\\xdaj\\xb2\\x83\\x9f\\x7f\\xc1#JlL\\x88\\x00\\x82\\x18\\xda\\xfd\\x98\\xc0R\\xfe\\x10K\\xdf&amp;gt;\\xdf\\xd3\\x1bh\\x87d&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Module: biobb_mem.ambertools.cpptraj_density Version: 5.0.4\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:82 /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556 directory successfully created\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/topology.pdb to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/data/ambertools/trajectory.xtc to /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:63 cpptraj -i 9f7a988f-9c0d-43cc-aeae-701860fdedd9/instructions.in\n\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:36 Executing: cpptraj -i 9f7a988f-9c0d-43cc-aeae-701860fdedd9/instructions.in...\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:cmd_wrapper.py:41 \nCPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)\n    ___  ___  ___  ___\n     | \\/ | \\/ | \\/ | \n    _|_/\\_|_/\\_|_/\\_|_\n\n| Date/time: 12/16/24 12:14:49\n| Available memory: 6.126 GB\n\nINPUT: Reading input from &amp;#x27;9f7a988f-9c0d-43cc-aeae-701860fdedd9/instructions.in&amp;#x27;\n  [parm /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/topology.pdb]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/topology.pdb&amp;#x27; as PDB File\n\tReading 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;topology.pdb&amp;#x27;.\n  [trajin /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/trajectory.xtc 5 15 1]\n\tReading &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/trajectory.xtc&amp;#x27; as Gromacs XTC\nWarning: Box X vector length is zero.\nWarning: Box Y vector length is zero.\nWarning: Box Z vector length is zero.\nWarning: stop 15 &amp;gt; #Frames (12), setting to max.\n  [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n    DENSITY: Determining mass density for 2 masks.\n\troutine version: 1.0.3\n\tDelta is 0.140000\n\tAxis is Y\n\tData set name is &amp;#x27;DENSITY_00001&amp;#x27;\n\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n\tBin coordinates will be to bin center.\n\tOutput to &amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/output.dat&amp;#x27;\n---------- RUN BEGIN -------------------------------------------------\n\nPARAMETER FILES (1 total):\n 0: topology.pdb, 47441 atoms, 2259 res, box: None, 599 mol\n\nINPUT TRAJECTORIES (1 total):\n 0: &amp;#x27;trajectory.xtc&amp;#x27; is a GROMACS XTC file, Parm topology.pdb (reading 8 of 12)\n  Coordinate processing will occur on 8 frames.\n\nBEGIN TRAJECTORY PROCESSING:\n.....................................................\nACTION SETUP FOR PARM &amp;#x27;topology.pdb&amp;#x27; (1 actions):\n  0: [density mass out /tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556/output.dat ::M,A,B ::A,B delta 0.14 y bincenter]\n\t [::M,A,B](36840)\n\t [::A,B](7140)\n----- trajectory.xtc (5-12, 1) -----\n 0% 14% 29% 43% 57% 71% 86% 100% Complete.\n\nRead 8 frames and processed 8 frames.\nTIME: Avg. throughput= 174.2654 frames / second.\n\nACTION OUTPUT:\n    DENSITY: The average box area in X/Z is 0.00 Angstrom (sd = 0.00).\nTIME: Analyses took 0.0000 seconds.\n\nDATASETS (4 total):\n\tDENSITY_00001[avg]:1 &amp;quot;::M,A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:1 &amp;quot;sd(::M,A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[avg]:2 &amp;quot;::A,B&amp;quot; (double), size is 1282 (10.256 kB)\n\tDENSITY_00001[sd]:2 &amp;quot;sd(::A,B)&amp;quot; (double), size is 1282 (10.256 kB)\n    Total data set memory usage is at least 41.024 kB\n\nDATAFILES (1 total):\n  output.dat (Standard Data File):  ::M,A,B sd(::M,A,B) ::A,B sd(::A,B)\n\nRUN TIMING:\nTIME:\t\tInit               : 0.0000 s (  0.01%)\nTIME:\t\tTrajectory Process : 0.0459 s ( 92.49%)\nTIME:\t\tAction Post        : 0.0001 s (  0.13%)\nTIME:\t\tAnalysis           : 0.0000 s (  0.00%)\nTIME:\t\tData File Write    : 0.0035 s (  7.13%)\nTIME:\t\tOther              : 0.0001 s (  0.00%)\nTIME:\tRun Total 0.0496 s\n---------- RUN END ---------------------------------------------------\nTIME: Total execution time: 0.1231 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_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_106/cpptraj_density_complex/sandbox_ccd25569-5f60-4917-a13b-3da5356a0556&amp;#x27;, &amp;#x27;9f7a988f-9c0d-43cc-aeae-701860fdedd9&amp;#x27;]\nINFO     /tmp/biobb/unitests_106/cpptraj_density_complex/cpptraj_density_complex_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_fatslim/test_fatslim_membranes.py::TestFatslimMembranescDefault::test_fatslim_membranes&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_fatslim/test_fatslim_membranes.py::TestFatslimMembranescDefault::test_fatslim_membranes&#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_mem/test/unitests/test_fatslim/test_fatslim_membranes.py::TestFatslimMembranescDefault::test_fatslim_membranes&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 -----------------------------\nWarning: trajectory probably has no box variable. Setting dimensions ussing the minimum and maximum positions of the atoms.\n\ncmd_wrapper commnand print: gmx editconf -f /tmp/biobb/unitests_106/fatslim_membranes/sandbox_6f9ee3f2-b95b-4200-ba89-c61924e5f365/A01JD.pdb -o 48ca44b3-26db-4eaf-848c-6d781bccb71b/output.gro -box 173.48001 168.94 122.75001 ; fatslim membranes -n 87a2c436-b0f7-457c-8162-182503ce091b/headgroups.ndx -c 48ca44b3-26db-4eaf-848c-6d781bccb71b/output.gro --output-index b8bb7e18-9216-46ef-830d-dd9ad0f5c721/output.ndx --cutoff 2.2 --begin-frame -1 --end-frame -1\nExecuting: gmx editconf -f /tmp/biobb/unitests_106/fatslim_membranes/sandbox_6f9ee3f2-b95b-...\nExit code: 0\n\nChecking if empty file: /tmp/biobb/unitests_106/fatslim_membranes/leaflets.ndx\nComparing: \n        File_A: /tmp/biobb/unitests_106/fatslim_membranes/leaflets.ndx\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/fatslim/leaflets.ndx\n        File_A hash: b&amp;#x27;\\xff\\x96\\xc2[\\x00\\\\\\xa4\\xe1\\xb2\\x82O&amp;amp;@\\t\\xc8MF&amp;quot;\\xeb\\xe9&amp;lt;\\x96\\&amp;#x27;\\x91\\xc9.\\x92\\x15Ih\\xad\\\\&amp;#x27;\n        File_B hash: b&amp;#x27;\\xff\\x96\\xc2[\\x00\\\\\\xa4\\xe1\\xb2\\x82O&amp;amp;@\\t\\xc8MF&amp;quot;\\xeb\\xe9&amp;lt;\\x96\\&amp;#x27;\\x91\\xc9.\\x92\\x15Ih\\xad\\\\&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_lipyphilic_biobb/test_lpp_assign_leaflets.py::TestLipyphilicLeafletsDefault::test_lipyphilic_leaflets_default&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_lipyphilic_biobb/test_lpp_assign_leaflets.py::TestLipyphilicLeafletsDefault::test_lipyphilic_leaflets_default&#34;, &#34;duration&#34;: &#34;556 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_mem/test/unitests/test_lipyphilic_biobb/test_lpp_assign_leaflets.py::TestLipyphilicLeafletsDefault::test_lipyphilic_leaflets_default&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;556 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 -----------------------------\nChecking if empty file: /tmp/biobb/unitests_106/lpp_assign_leaflets/leaflets_data.csv\nComparing: \n        File_A: /tmp/biobb/unitests_106/lpp_assign_leaflets/leaflets_data.csv\n        File_B: /home/user/actions-runner/_work/biobb_mem/biobb_mem/biobb_mem/test/reference/lipyphilic_biobb/leaflets_data.csv\n        File_A hash: b&amp;#x27;\\x87\\xc7\\x9c\\xcf\\xc3Y4P2\\x02\\xad:\\x06\\xc0O&amp;lt;\\xf9U/-\\x1e\\xf3\\xcf\\x7f@\\xea\\x19#\\x05\\xcc\\x05C&amp;#x27;\n        File_B hash: b&amp;#x27;\\x87\\xc7\\x9c\\xcf\\xc3Y4P2\\x02\\xad:\\x06\\xc0O&amp;lt;\\xf9U/-\\x1e\\xf3\\xcf\\x7f@\\xea\\x19#\\x05\\xcc\\x05C&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_lipyphilic_biobb/test_lpp_zpositions.py::TestLipyphilicPositionsDefault::test_lipyphilic_positons_default&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_lipyphilic_biobb/test_lpp_zpositions.py::TestLipyphilicPositionsDefault::test_lipyphilic_positons_default&#34;, &#34;duration&#34;: &#34;557 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_mem/test/unitests/test_lipyphilic_biobb/test_lpp_zpositions.py::TestLipyphilicPositionsDefault::test_lipyphilic_positons_default&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;557 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 -----------------------------\nChecking if empty file: /tmp/biobb/unitests_106/lpp_zpositions/zpositions.csv\nComparing: \n        File_A: /tmp/biobb/unitests_106/lpp_zpositions/zpositions.csv\n        File_B: /tmp/biobb/unitests_106/lpp_zpositions/zpositions.csv\n        File_A hash: b&amp;#x27;&amp;lt;Gm\\x12\\x17\\xca\\x88\\xdb\\x12\\x8bH\\xb3\\x85V\\xfc\\xb6\\xd9\\x89FAm\\xb0\\xddK\\x90\\xb9\\xe3N\\xa7\\xbe@\\x8f&amp;#x27;\n        File_B hash: b&amp;#x27;&amp;lt;Gm\\x12\\x17\\xca\\x88\\xdb\\x12\\x8bH\\xb3\\x85V\\xfc\\xb6\\xd9\\x89FAm\\xb0\\xddK\\x90\\xb9\\xe3N\\xa7\\xbe@\\x8f&amp;#x27;\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_106\n&#34;}], &#34;biobb_mem/test/unitests/test_mdanalysis_biobb/test_mdanalays_biobb.py::TestMDAHole::test_mda_hole_default&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_mem/test/unitests/test_mdanalysis_biobb/test_mdanalays_biobb.py::TestMDAHole::test_mda_hole_default&#34;, &#34;duration&#34;: &#34;00:00:06&#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_mem/test/unitests/test_mdanalysis_biobb/test_mdanalays_biobb.py::TestMDAHole::test_mda_hole_default&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_106/mda_hole/hole.vmd\nComparing size of both files:\n     FILE_A: 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