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Updating workflows/bacterial_genomics/bacterial_genome_annotation from 1.1.11 to 1.1.12 #978

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Updating workflows/bacterial_genomics/bacterial_genome_annotation from 1.1.11 to 1.1.12 #978

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Hello! This is an automated update of the following workflow: workflows/bacterial_genomics/bacterial_genome_annotation. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

  • toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.1+galaxy0
  • toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.1+galaxy0

The workflow release number has been updated from 1.1.11 to 1.1.12.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

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github-actions bot commented Oct 7, 2025

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ bacterial_genome_annotation.ga_0

    Workflow invocation details

    • Invocation Messages

    • Steps

      • Step 1: Input sequence fasta:

        • step_state: scheduled

      • Step 2: Select a plasmid detection database:

        • step_state: scheduled

      • Step 3: Select a bacterial genome annotation database:

        • step_state: scheduled

      • Step 4: Select a AMRFinderPlus database:

        • step_state: scheduled

      • Step 5: genomic_annotation_insertionelement_isescan:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat' input && isescan.py --seqfile input --output 'results'  --nthread ${GALAXY_SLOTS:-7}  | tee '/tmp/tmpxt_eqome/job_working_directory/000/2/outputs/dataset_8791e291-767b-43ba-a655-39fb89cc5f1c.dat'

            Exit Code:

            • 0

            Standard Output:

            • /usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1
Using 1 threads.
no. of seqs: 153
Clock time used (by 1 threads) = 3.1 sec
Time elapsed: 0 hours 0 minutes and 3 seconds.
ISEScan starts at Tue Oct  7 15:41:46 2025
predict and translate genes from genome sequence into protein database using FragGeneScan program

Begin to translate genome into proteome.
Translating genome into proteome for input , return  0

Finish translating genome into proteome. Tue Oct  7 15:41:49 2025

Begin to phmmer search against proteome database. Tue Oct  7 15:41:49 2025
Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa  against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa

Finish phmmer searching against proteome database. Tue Oct  7 15:52:23 2025

Begin to profile HMM search against proteome database. Tue Oct  7 15:52:23 2025
Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm  against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa

Finish profile HMM searching against proteome database. Tue Oct  7 16:02:04 2025
pred begins at Tue Oct  7 16:02:04 2025
Warning: no significant hit with E-value <= 1e-10 found for contig00002
Warning: no significant hit with E-value <= 1e-10 found for contig00003
Warning: no significant hit with E-value <= 1e-10 found for contig00004
Warning: no significant hit with E-value <= 1e-10 found for contig00005
Warning: no significant hit with E-value <= 1e-10 found for contig00006
Warning: no significant hit with E-value <= 1e-10 found for contig00008
Warning: no significant hit with E-value <= 1e-10 found for contig00011
Warning: no significant hit with E-value <= 1e-10 found for contig00012
Warning: no significant hit with E-value <= 1e-10 found for contig00013
Warning: no significant hit with E-value <= 1e-10 found for contig00014
Warning: no significant hit with E-value <= 1e-10 found for contig00017
Warning: no significant hit with E-value <= 1e-10 found for contig00020
Warning: no significant hit with E-value <= 1e-10 found for contig00021
Warning: no significant hit with E-value <= 1e-10 found for contig00022
Warning: no significant hit with E-value <= 1e-10 found for contig00023
Warning: no significant hit with E-value <= 1e-10 found for contig00024
Warning: no significant hit with E-value <= 1e-10 found for contig00026
Warning: no significant hit with E-value <= 1e-10 found for contig00027
Warning: no significant hit with E-value <= 1e-10 found for contig00028
Warning: no significant hit with E-value <= 1e-10 found for contig00030
Warning: no significant hit with E-value <= 1e-10 found for contig00031
Warning: no significant hit with E-value <= 1e-10 found for contig00032
Warning: no significant hit with E-value <= 1e-10 found for contig00033
Warning: no significant hit with E-value <= 1e-10 found for contig00034
Warning: no significant hit with E-value <= 1e-10 found for contig00035
Warning: no significant hit with E-value <= 1e-10 found for contig00036
Warning: no significant hit with E-value <= 1e-10 found for contig00037
Warning: no significant hit with E-value <= 1e-10 found for contig00040
Warning: no significant hit with E-value <= 1e-10 found for contig00041
Warning: no significant hit with E-value <= 1e-10 found for contig00042
Warning: no significant hit with E-value <= 1e-10 found for contig00044
Warning: no significant hit with E-value <= 1e-10 found for contig00045
Warning: no significant hit with E-value <= 1e-10 found for contig00046
Warning: no significant hit with E-value <= 1e-10 found for contig00047
Warning: no significant hit with E-value <= 1e-10 found for contig00048
Warning: no significant hit with E-value <= 1e-10 found for contig00050
Warning: no significant hit with E-value <= 1e-10 found for contig00051
Warning: no significant hit with E-value <= 1e-10 found for contig00053
Warning: no significant hit with E-value <= 1e-10 found for contig00054
Warning: no significant hit with E-value <= 1e-10 found for contig00055
Warning: no significant hit with E-value <= 1e-10 found for contig00057
Warning: no significant hit with E-value <= 1e-10 found for contig00058
Warning: no significant hit with E-value <= 1e-10 found for contig00059
Warning: no significant hit with E-value <= 1e-10 found for contig00060
Warning: no significant hit with E-value <= 1e-10 found for contig00061
Warning: no significant hit with E-value <= 1e-10 found for contig00063
Warning: no significant hit with E-value <= 1e-10 found for contig00064
Warning: no significant hit with E-value <= 1e-10 found for contig00065
Warning: no significant hit with E-value <= 1e-10 found for contig00066
Warning: no significant hit with E-value <= 1e-10 found for contig00068
Warning: no significant hit with E-value <= 1e-10 found for contig00069
Warning: no significant hit with E-value <= 1e-10 found for contig00070
Warning: no significant hit with E-value <= 1e-10 found for contig00072
Warning: no significant hit with E-value <= 1e-10 found for contig00073
Warning: no significant hit with E-value <= 1e-10 found for contig00074
Warning: no significant hit with E-value <= 1e-10 found for contig00075
Warning: no significant hit with E-value <= 1e-10 found for contig00076
Warning: no significant hit with E-value <= 1e-10 found for contig00077
Warning: no significant hit with E-value <= 1e-10 found for contig00078
Warning: no significant hit with E-value <= 1e-10 found for contig00083
Warning: no significant hit with E-value <= 1e-10 found for contig00084
Warning: no significant hit with E-value <= 1e-10 found for contig00085
Warning: no significant hit with E-value <= 1e-10 found for contig00086
Warning: no significant hit with E-value <= 1e-10 found for contig00087
Warning: no significant hit with E-value <= 1e-10 found for contig00089
Warning: no significant hit with E-value <= 1e-10 found for contig00090
Warning: no significant hit with E-value <= 1e-10 found for contig00091
Warning: no significant hit with E-value <= 1e-10 found for contig00092
Warning: no significant hit with E-value <= 1e-10 found for contig00094
Warning: no significant hit with E-value <= 1e-10 found for contig00096
Warning: no significant hit with E-value <= 1e-10 found for contig00097
Warning: no significant hit with E-value <= 1e-10 found for contig00101
Warning: no significant hit with E-value <= 1e-10 found for contig00102
Warning: no significant hit with E-value <= 1e-10 found for contig00103
Warning: no significant hit with E-value <= 1e-10 found for contig00105
Warning: no significant hit with E-value <= 1e-10 found for contig00106
Warning: no significant hit with E-value <= 1e-10 found for contig00110
Warning: no significant hit with E-value <= 1e-10 found for contig00112
Warning: no significant hit with E-value <= 1e-10 found for contig00113
Warning: no significant hit with E-value <= 1e-10 found for contig00116
Warning: no significant hit with E-value <= 1e-10 found for contig00117
Warning: no significant hit with E-value <= 1e-10 found for contig00119
Warning: no significant hit with E-value <= 1e-10 found for contig00120
Warning: no significant hit with E-value <= 1e-10 found for contig00121
Warning: no significant hit with E-value <= 1e-10 found for contig00122
Warning: no significant hit with E-value <= 1e-10 found for contig00128
Warning: no significant hit with E-value <= 1e-10 found for contig00129
Warning: no significant hit with E-value <= 1e-10 found for contig00133
Warning: no significant hit with E-value <= 1e-10 found for contig00135
Warning: no significant hit with E-value <= 1e-10 found for contig00139
Warning: no significant hit with E-value <= 1e-10 found for contig00140
Warning: no significant hit with E-value <= 1e-10 found for contig00141
Warning: no significant hit with E-value <= 1e-10 found for contig00143
Warning: no significant hit with E-value <= 1e-10 found for contig00144
Warning: no significant hit with E-value <= 1e-10 found for contig00146
Warning: no significant hit with E-value <= 1e-10 found for contig00149
Begin addNonORFcopy at Tue Oct  7 16:02:09 2025
Finish addNonORFcopy at Tue Oct  7 16:02:09 2025
Begin addNonORFcopy1 at Tue Oct  7 16:02:13 2025
Finish addNonORFcopy1 at Tue Oct  7 16:02:13 2025
getFullIS() begins at Tue Oct  7 16:02:13 2025
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 -32-268 around ORF (('contig00007', 2, 118, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00007', 2, 118, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 66624-66924 66740-66891 around ORF (('contig00007', 66774, 66890, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00007', 66774, 66890, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 73-373 around ORF (('contig00039', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 1, {'orfhits4tpase': [(('contig00039', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 33095-33395 33308-33459 around ORF (('contig00039', 33245, 33458, '+'), 'new_167|new||protein:plasmid:131871', 2.6e-15, 2.6e-15, 1, {'orfhits4tpase': [(('contig00039', 33245, 33458, '+'), 'new_167|new||protein:plasmid:131871', 2.6e-15, 2.6e-15, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 5406-5706 5519-5819 around ORF (('contig00043', 5556, 5669, '-'), 'IS3_206', 3.3e-15, 3.3e-15, 1, {'orfhits4tpase': [(('contig00043', 5556, 5669, '-'), 'IS3_206', 3.3e-15, 3.3e-15, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 23685-23985 23801-23952 around ORF (('contig00049', 23835, 23951, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00049', 23835, 23951, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 117-417 around ORF (('contig00062', 3, 267, '-'), 'IS6_292', 4.6e-12, 4.6e-12, 1, {'orfhits4tpase': [(('contig00062', 3, 267, '-'), 'IS6_292', 4.6e-12, 4.6e-12, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 124-424 387-687 around ORF (('contig00062', 274, 537, '-'), 'IS6_292', 1.4e-45, 1.4e-45, 1, {'orfhits4tpase': [(('contig00062', 274, 537, '-'), 'IS6_292', 1.4e-45, 1.4e-45, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 -15-285 around ORF (('contig00079', 1, 135, '+'), 'IS256_162', 1.9e-13, 1.9e-13, 1, {'orfhits4tpase': [(('contig00079', 1, 135, '+'), 'IS256_162', 1.9e-13, 1.9e-13, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 54-354 around ORF (('contig00081', 1, 204, '+'), 'IS256_162', 1.1e-12, 1.1e-12, 1, {'orfhits4tpase': [(('contig00081', 1, 204, '+'), 'IS256_162', 1.1e-12, 1.1e-12, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 8293-8593 8547-8847 around ORF (('contig00082', 8443, 8697, '-'), 'IS256_128', 1.9e-28, 1.9e-28, 1, {'orfhits4tpase': [(('contig00082', 8443, 8697, '-'), 'IS256_128', 1.9e-28, 1.9e-28, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 -33-267 around ORF (('contig00093', 1, 117, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00093', 1, 117, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 2055-2355 2189-2342 around ORF (('contig00100', 2205, 2339, '+'), 'IS6_292', 4.9e-21, 4.9e-21, 1, {'orfhits4tpase': [(('contig00100', 2205, 2339, '+'), 'IS6_292', 4.9e-21, 4.9e-21, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 147-300 around ORF (('contig00130', 1, 297, '+'), 'IS30_241', 3.5e-50, 3.5e-50, 1, {'orfhits4tpase': [(('contig00130', 1, 297, '+'), 'IS30_241', 3.5e-50, 3.5e-50, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 104-255 around ORF (('contig00136', 3, 254, '+'), 'IS6_292', 1.4e-46, 1.4e-46, 1, {'orfhits4tpase': [(('contig00136', 3, 254, '+'), 'IS6_292', 1.4e-46, 1.4e-46, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 104-255 around ORF (('contig00137', 3, 254, '+'), 'IS30_241', 1.2e-41, 1.2e-41, 1, {'orfhits4tpase': [(('contig00137', 3, 254, '+'), 'IS30_241', 1.2e-41, 1.2e-41, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 73-255 around ORF (('contig00138', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 1, {'orfhits4tpase': [(('contig00138', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 98-249 around ORF (('contig00145', 3, 248, '-'), 'IS6_292', 1.4e-34, 1.4e-34, 1, {'orfhits4tpase': [(('contig00145', 3, 248, '-'), 'IS6_292', 1.4e-34, 1.4e-34, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 79-231 around ORF (('contig00147', 2, 229, '-'), 'IS6_292', 4.6e-41, 4.6e-41, 1, {'orfhits4tpase': [(('contig00147', 2, 229, '-'), 'IS6_292', 4.6e-41, 4.6e-41, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 -2-151 around ORF (('contig00150', 2, 148, '-'), 'IS6_292', 8.7e-25, 8.7e-25, 1, {'orfhits4tpase': [(('contig00150', 2, 148, '-'), 'IS6_292', 8.7e-25, 8.7e-25, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 -32-618 around ORF (('contig00007', 2, 118, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00007', 2, 118, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 66274-66924 66740-66891 around ORF (('contig00007', 66774, 66890, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00007', 66774, 66890, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 73-723 around ORF (('contig00039', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 1, {'orfhits4tpase': [(('contig00039', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 32745-33395 33308-33459 around ORF (('contig00039', 33245, 33458, '+'), 'new_167|new||protein:plasmid:131871', 2.6e-15, 2.6e-15, 1, {'orfhits4tpase': [(('contig00039', 33245, 33458, '+'), 'new_167|new||protein:plasmid:131871', 2.6e-15, 2.6e-15, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 5056-5706 5519-6169 around ORF (('contig00043', 5556, 5669, '-'), 'IS3_206', 3.3e-15, 3.3e-15, 1, {'orfhits4tpase': [(('contig00043', 5556, 5669, '-'), 'IS3_206', 3.3e-15, 3.3e-15, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 23335-23985 23801-23952 around ORF (('contig00049', 23835, 23951, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00049', 23835, 23951, '-'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 117-767 around ORF (('contig00062', 3, 267, '-'), 'IS6_292', 4.6e-12, 4.6e-12, 1, {'orfhits4tpase': [(('contig00062', 3, 267, '-'), 'IS6_292', 4.6e-12, 4.6e-12, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-424 387-1037 around ORF (('contig00062', 274, 537, '-'), 'IS6_292', 1.4e-45, 1.4e-45, 1, {'orfhits4tpase': [(('contig00062', 274, 537, '-'), 'IS6_292', 1.4e-45, 1.4e-45, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 -15-635 around ORF (('contig00079', 1, 135, '+'), 'IS256_162', 1.9e-13, 1.9e-13, 1, {'orfhits4tpase': [(('contig00079', 1, 135, '+'), 'IS256_162', 1.9e-13, 1.9e-13, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 54-704 around ORF (('contig00081', 1, 204, '+'), 'IS256_162', 1.1e-12, 1.1e-12, 1, {'orfhits4tpase': [(('contig00081', 1, 204, '+'), 'IS256_162', 1.1e-12, 1.1e-12, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 7943-8593 8547-8939 around ORF (('contig00082', 8443, 8697, '-'), 'IS256_128', 1.9e-28, 1.9e-28, 1, {'orfhits4tpase': [(('contig00082', 8443, 8697, '-'), 'IS256_128', 1.9e-28, 1.9e-28, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 -33-617 around ORF (('contig00093', 1, 117, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 1, {'orfhits4tpase': [(('contig00093', 1, 117, '+'), 'IS30_241', 4.7e-11, 4.7e-11, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1705-2355 2189-2342 around ORF (('contig00100', 2205, 2339, '+'), 'IS6_292', 4.9e-21, 4.9e-21, 1, {'orfhits4tpase': [(('contig00100', 2205, 2339, '+'), 'IS6_292', 4.9e-21, 4.9e-21, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-151 147-300 around ORF (('contig00130', 1, 297, '+'), 'IS30_241', 3.5e-50, 3.5e-50, 1, {'orfhits4tpase': [(('contig00130', 1, 297, '+'), 'IS30_241', 3.5e-50, 3.5e-50, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 104-255 around ORF (('contig00136', 3, 254, '+'), 'IS6_292', 1.4e-46, 1.4e-46, 1, {'orfhits4tpase': [(('contig00136', 3, 254, '+'), 'IS6_292', 1.4e-46, 1.4e-46, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 104-255 around ORF (('contig00137', 3, 254, '+'), 'IS30_241', 1.2e-41, 1.2e-41, 1, {'orfhits4tpase': [(('contig00137', 3, 254, '+'), 'IS30_241', 1.2e-41, 1.2e-41, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 73-255 around ORF (('contig00138', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 1, {'orfhits4tpase': [(('contig00138', 2, 223, '-'), 'IS30_241', 8.5e-32, 8.5e-32, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-153 98-249 around ORF (('contig00145', 3, 248, '-'), 'IS6_292', 1.4e-34, 1.4e-34, 1, {'orfhits4tpase': [(('contig00145', 3, 248, '-'), 'IS6_292', 1.4e-34, 1.4e-34, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 79-231 around ORF (('contig00147', 2, 229, '-'), 'IS6_292', 4.6e-41, 4.6e-41, 1, {'orfhits4tpase': [(('contig00147', 2, 229, '-'), 'IS6_292', 4.6e-41, 4.6e-41, 0)]})
No tir will be found in the invalid tir search window (org= fastafile=input): 1-152 -2-151 around ORF (('contig00150', 2, 148, '-'), 'IS6_292', 8.7e-25, 8.7e-25, 1, {'orfhits4tpase': [(('contig00150', 2, 148, '-'), 'IS6_292', 8.7e-25, 8.7e-25, 0)]})
Start typing IS elements
Warning: no valid hit found for contig00001
The partial IS element with isLen < 1027: isLen=117 IS30 bd=[2, 118] orf('contig00007', 2, 118, '+') evalue=4.7e-11
The partial IS element with isLen < 1027: isLen=117 IS30 bd=[66774, 66890] orf('contig00007', 66774, 66890, '-') evalue=4.7e-11
The single-copy partial IS element with evalue > 1e-50: isLen=1715 ISL3 bd=[88, 1802] orf('contig00009', 187, 1613, '+') evalue=1.4e-44
The partial IS element with isLen < 1924: isLen=1542 IS21 bd=[46818, 48359] orf('contig00010', 46976, 48319, '+') evalue=6.5e-15
Warning: no valid hit found for contig00015
Warning: no valid hit found for contig00016
Warning: no valid hit found for contig00018
Warning: no valid hit found for contig00019
Warning: no valid hit found for contig00025
The partial IS element with isLen < 1924: isLen=1849 IS21 bd=[5545, 7393] orf('contig00029', 5881, 7182, '-') evalue=5.5e-13
Warning: no valid hit found for contig00038
The partial IS element with isLen < 1027: isLen=222 IS30 bd=[2, 223] orf('contig00039', 2, 223, '-') evalue=8.5e-32
The single-copy partial IS element with evalue > 1e-50: isLen=1725 IS3 bd=[5464, 7188] orf('contig00043', 5673, 7113, '-') evalue=4.4e-18
The partial IS element with isLen < 435: isLen=114 IS3 bd=[5556, 5669] orf('contig00043', 5556, 5669, '-') evalue=3.3e-15
The partial IS element with isLen < 1027: isLen=117 IS30 bd=[23835, 23951] orf('contig00049', 23835, 23951, '-') evalue=4.7e-11
Warning: no valid hit found for contig00052
Warning: no valid hit found for contig00056
The partial IS element with isLen < 696: isLen=265 IS6 bd=[3, 267] orf('contig00062', 3, 267, '-') evalue=4.6e-12
The partial IS element with isLen < 696: isLen=264 IS6 bd=[274, 537] orf('contig00062', 274, 537, '-') evalue=1.4e-45
The single-copy partial IS element with evalue > 1e-50: isLen=993 IS630 bd=[12189, 13181] orf('contig00067', 12162, 12867, '+') evalue=2.8e-12
The partial IS element with isLen < 1124: isLen=135 IS256 bd=[1, 135] orf('contig00079', 1, 135, '+') evalue=1.9e-13
Warning: no valid hit found for contig00080
The partial IS element with isLen < 1124: isLen=204 IS256 bd=[1, 204] orf('contig00081', 1, 204, '+') evalue=1.1e-12
The single-copy partial IS element with evalue > 1e-50: isLen=1546 ISL3 bd=[1334, 2879] orf('contig00081', 1766, 2566, '-') evalue=1.8e-48
The single-copy partial IS element with evalue > 1e-50: isLen=1476 IS3 bd=[6690, 8165] orf('contig00081', 6742, 8206, '+') evalue=1.5e-20
The partial IS element with isLen < 1124: isLen=255 IS256 bd=[8443, 8697] orf('contig00082', 8443, 8697, '-') evalue=1.9e-28
Warning: no valid hit found for contig00088
The partial IS element with isLen < 1027: isLen=117 IS30 bd=[1, 117] orf('contig00093', 1, 117, '+') evalue=4.7e-11
The partial IS element with isLen < 1124: isLen=649 IS256 bd=[1683, 2331] orf('contig00098', 1792, 2451, '+') evalue=4.1e-99
Warning: no valid hit found for contig00099
The partial IS element with isLen < 696: isLen=135 IS6 bd=[2205, 2339] orf('contig00100', 2205, 2339, '+') evalue=4.9e-21
The single-copy partial IS element with evalue > 1e-50: isLen=1353 IS110 bd=[163, 1515] orf('contig00104', 141, 1391, '-') evalue=1e-33
The single-copy partial IS element with evalue > 1e-50: isLen=1404 ISL3 bd=[75, 1478] orf('contig00107', 84, 1367, '-') evalue=2.1e-50
The partial IS element with isLen < 1027: isLen=491 IS30 bd=[102, 592] orf('contig00114', 1, 651, '+') evalue=6.2e-113
The partial IS element with isLen < 1124: isLen=612 IS256 bd=[12, 623] orf('contig00115', 1, 648, '+') evalue=2.4e-108
The partial IS element with isLen < 1124: isLen=429 IS256 bd=[11, 439] orf('contig00118', 3, 443, '-') evalue=1.5e-63
The partial IS element with isLen < 1027: isLen=130 IS30 bd=[110, 239] orf('contig00125', 10, 345, '-') evalue=1.7e-50
The partial IS element with isLen < 1124: isLen=238 IS256 bd=[23, 260] orf('contig00126', 2, 337, '-') evalue=8.8e-54
The partial IS element with isLen < 1027: isLen=297 IS30 bd=[1, 297] orf('contig00130', 1, 297, '+') evalue=3.5e-50
The partial IS element with isLen < 696: isLen=252 IS6 bd=[3, 254] orf('contig00136', 3, 254, '+') evalue=1.4e-46
The partial IS element with isLen < 1027: isLen=252 IS30 bd=[3, 254] orf('contig00137', 3, 254, '+') evalue=1.2e-41
The partial IS element with isLen < 1027: isLen=222 IS30 bd=[2, 223] orf('contig00138', 2, 223, '-') evalue=8.5e-32
The partial IS element with isLen < 696: isLen=246 IS6 bd=[3, 248] orf('contig00145', 3, 248, '-') evalue=1.4e-34
The partial IS element with isLen < 696: isLen=228 IS6 bd=[2, 229] orf('contig00147', 2, 229, '-') evalue=4.6e-41
The partial IS element with isLen < 696: isLen=147 IS6 bd=[2, 148] orf('contig00150', 2, 148, '-') evalue=8.7e-25
Warning: no valid hit after removing short IS element candidate for contig00001
Warning: no valid hit after removing short IS element candidate for contig00015
Warning: no valid hit after removing short IS element candidate for contig00016
Warning: no valid hit after removing short IS element candidate for contig00018
Warning: no valid hit after removing short IS element candidate for contig00019
Warning: no valid hit after removing short IS element candidate for contig00025
Warning: no valid hit after removing short IS element candidate for contig00038
Warning: no valid hit after removing short IS element candidate for contig00052
Warning: no valid hit after removing short IS element candidate for contig00056
Warning: no valid hit after removing short IS element candidate for contig00080
Warning: no valid hit after removing short IS element candidate for contig00088
Warning: no valid hit after removing short IS element candidate for contig00099
Finish typing partial IS elements
Begin removeOverlappedHits at Tue Oct  7 16:02:13 2025
contig00007: no intersected hits found
contig00009: no intersected hits found
contig00010: no intersected hits found
contig00029: no intersected hits found
contig00039: no intersected hits found
contig00043: 2 intersected hits found, do clustering to pick the representative hit for each cluster
contig00049: no intersected hits found
contig00062: no intersected hits found
contig00067: no intersected hits found
contig00071: no intersected hits found
contig00079: no intersected hits found
contig00081: no intersected hits found
contig00082: no intersected hits found
contig00093: no intersected hits found
contig00095: no intersected hits found
contig00098: no intersected hits found
contig00100: no intersected hits found
contig00104: no intersected hits found
contig00107: no intersected hits found
contig00108: no intersected hits found
contig00111: no intersected hits found
contig00114: no intersected hits found
contig00115: no intersected hits found
contig00118: no intersected hits found
contig00125: no intersected hits found
contig00126: no intersected hits found
contig00130: no intersected hits found
contig00136: no intersected hits found
contig00137: no intersected hits found
contig00138: no intersected hits found
contig00145: no intersected hits found
contig00147: no intersected hits found
contig00150: no intersected hits found
Finish removeOverlappedHits at Tue Oct  7 16:02:13 2025
Begin reading protein database at Tue Oct  7 16:02:13 2025
Finish reading protein database at Tue Oct  7 16:02:13 2025
Write IS elements from all sequences in input into one result file under results
Write 40 IS copies to results/input.csv and results/input.tsv and results/input.raw
Write summarized result to results/input.sum
End in pred Tue Oct  7 16:02:13 2025
Both complete and partial IS elements are reported.
ISEScan ends at Tue Oct  7 16:02:13 2025

            Traceback:

            • 

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e6c3eaaaa39311f0a35e0022480b3a6c"

              

              
chromInfo
"/tmp/tmpxt_eqome/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
log_activate
true

              

              
remove_short_is
false

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 6: genomic_annotation_integron:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              integron_finder '/tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat' --cpu ${GALAXY_SLOTS:-2} --keep-tmp --local-max --promoter-attI -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40       && mv Results_Integron_Finder_* Results_Integron_Finder
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              **************************************************************************
 ___       _                               _____ _           _
|_ _|_ __ | |_ ___  __ _ _ __ ___  _ __   |  ___(_)_ __   __| | ___ _ __
 | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \  | |_  | | '_ \ / _` |/ _ \ '__|
 | || | | | ||  __/ (_| | | | (_) | | | | |  _| | | | | | (_| |  __/ |
|___|_| |_|\__\___|\__, |_|  \___/|_| |_| |_|   |_|_| |_|\__,_|\___|_|
                   |___/

**************************************************************************

integron_finder version 2.0.5 
Using:
 - Python 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
 - numpy 1.26.4
 - pandas 2.2.2
 - matplolib 3.8.4
 - biopython 1.83

 - Prodigal V2.6.3: February, 2016
 - INFERNAL 1.1.4 (Dec 2020)
 - HMMER 3.3.2 (Nov 2020); http://hmmer.org/

Authors:
 - Jean Cury, Bertrand Neron, Eduardo Rocha,

Citation:

 Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C. 
 IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. 
 Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700

 If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite

 Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
 PMID: 29112715
 

                     =======================

integron_finder is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

integron_finder is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program (COPYING file).
If not, see <http://www.gnu.org/licenses/>.

                     =======================

command used: integron_finder /tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat --cpu 1 --keep-tmp --local-max --promoter-attI -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40

                     =======================

�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00001 (1/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00001, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00001, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00001�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00002 (2/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00002, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00002, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00002�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00003 (3/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00003, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00003, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00003�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00004 (4/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00004, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00004, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00004�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00005 (5/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00005, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00005, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00005�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00006 (6/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00006, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00006, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00006�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00007 (7/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00007, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00007, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00007�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00008 (8/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00008, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00008, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00008�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00009 (9/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00009, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 1 CALIN element(s) found with a total of 1 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m 	searched 45496->49696 in top strand(s) found 0 attc sites�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00009, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 1 CALIN element(s) found with a total of 2 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Adding proteins ... :�[0m
�[32mINFO     : �[0m Adding promoters and attI ... :�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00009�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00010 (10/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00010, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00010, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00010�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00011 (11/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00011, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00011, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00011�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00012 (12/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00012, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00012, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00012�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00013 (13/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00013, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00013, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00013�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00014 (14/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00014, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00014, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     
..
 Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00134, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00134, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00134�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00135 (135/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00135, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00135, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00135�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00136 (136/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00136, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00136, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00136�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00137 (137/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00137, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00137, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00137�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00138 (138/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00138, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00138, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00138�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00139 (139/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00139, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00139, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00139�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00140 (140/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00140, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00140, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00140�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00141 (141/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00141, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00141, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00141�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00142 (142/153) ############
�[0m
�[33mWARNING  : �[0m The protein file: '/tmp/tmpxt_eqome/job_working_directory/000/3/working/Results_Integron_Finder_dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3/tmp_contig00142/contig00142.prt' is empty cannot perform hmmsearch on it.�[0m
�[33mWARNING  : �[0m ############ Skip replicon contig00142 ############�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00143 (143/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00143, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00143, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00143�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00144 (144/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00144, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00144, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00144�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00145 (145/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00145, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00145, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00145�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00146 (146/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00146, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00146, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00146�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00147 (147/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00147, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00147, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00147�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00148 (148/153) ############
�[0m
�[33mWARNING  : �[0m The protein file: '/tmp/tmpxt_eqome/job_working_directory/000/3/working/Results_Integron_Finder_dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3/tmp_contig00148/contig00148.prt' is empty cannot perform hmmsearch on it.�[0m
�[33mWARNING  : �[0m ############ Skip replicon contig00148 ############�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00149 (149/153) ############
�[0m
�[33mWARNING  : �[0m The protein file: '/tmp/tmpxt_eqome/job_working_directory/000/3/working/Results_Integron_Finder_dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3/tmp_contig00149/contig00149.prt' is empty cannot perform hmmsearch on it.�[0m
�[33mWARNING  : �[0m ############ Skip replicon contig00149 ############�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00150 (150/153) ############
�[0m
�[32mINFO     : �[0m Starting Default search ... :�[0m
�[32mINFO     : �[0m Default search done... : �[0m
�[32mINFO     : �[0m In replicon contig00150, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Starting search with local_max...:�[0m
�[32mINFO     : �[0m Search with local_max done... :�[0m
�[32mINFO     : �[0m In replicon contig00150, there are:�[0m
�[32mINFO     : �[0m - 0 complete integron(s) found with a total 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 CALIN element(s) found with a total of 0 attC site(s)�[0m
�[32mINFO     : �[0m - 0 In0 element(s) found with a total of 0 attC site�[0m
�[32mINFO     : �[0m Writing out results for replicon contig00150�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00151 (151/153) ############
�[0m
�[33mWARNING  : �[0m The protein file: '/tmp/tmpxt_eqome/job_working_directory/000/3/working/Results_Integron_Finder_dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3/tmp_contig00151/contig00151.prt' is empty cannot perform hmmsearch on it.�[0m
�[33mWARNING  : �[0m ############ Skip replicon contig00151 ############�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00152 (152/153) ############
�[0m
�[33mWARNING  : �[0m The protein file: '/tmp/tmpxt_eqome/job_working_directory/000/3/working/Results_Integron_Finder_dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3/tmp_contig00152/contig00152.prt' is empty cannot perform hmmsearch on it.�[0m
�[33mWARNING  : �[0m ############ Skip replicon contig00152 ############�[0m
�[32mINFO     : �[0m ############ Processing replicon contig00153 (153/153) ############
�[0m
�[33mWARNING  : �[0m The protein file: '/tmp/tmpxt_eqome/job_working_directory/000/3/working/Results_Integron_Finder_dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3/tmp_contig00153/contig00153.prt' is empty cannot perform hmmsearch on it.�[0m
�[33mWARNING  : �[0m ############ Skip replicon contig00153 ############�[0m
�[32mINFO     : �[0m Merging integrons results.
�[0m

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e6c3eaaaa39311f0a35e0022480b3a6c"

              

              
chromInfo
"/tmp/tmpxt_eqome/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
gbk
false

              

              
local_max
true

              

              
no_logfile
false

              

              
pdf
false

              

              
promoter_attI
true

              

              
settings
{"attc_settings": {"calin_threshold": "2", "covar_matrix": null, "dist_thresh": "4000", "keep_palindromes": false, "max_attc_size": "200", "min_attc_size": "40"}, "protein_settings": {"func_annot": false, "no_proteins": false, "union_integrases": false}}

              

              
topology_file
None

              

              
type_replicon
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 7: genomic_annotation_plasmid_plasmidfinder:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              mkdir output_dir && mkdir temp_dir && plasmidfinder.py -i '/tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat' -p '/cvmfs/data.galaxyproject.org/byhand/plasmidfinder-db/81c11f4_2023_12_04' -l '0.6' -t '0.95' -mp blastn -x -o output_dir -tmp temp_dir | tee 'XXXX'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              Found: rep22_1b_repB(pAMalpha1)_AF503772
Saving: contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530:1166..1957:rep22_1b_repB(pAMalpha1)_AF503772:78.805970
Found: repUS12_1_rep(pUB110)_AF181950
Same contig: contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530
	repUS12_1_rep(pUB110)_AF181950 vs rep22_1b_repB(pAMalpha1)_AF503772
	overlap found (791): repUS12_1_rep(pUB110)_AF181950
Found: repUS12_2_repB(SAP014A)_GQ900379
Same contig: contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530
	repUS12_2_repB(SAP014A)_GQ900379 vs rep22_1b_repB(pAMalpha1)_AF503772
	overlap found (770): repUS12_2_repB(SAP014A)_GQ900379
	791 <= 1561
		Scores: 88.01369863013699 cmp 78.80597014925374
Saving: contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530:1187..1957:repUS12_2_repB(SAP014A)_GQ900379:88.013699
Found: rep22_1a_repB(pUB110)_X03408
Same contig: contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530
	rep22_1a_repB(pUB110)_X03408 vs repUS12_2_repB(SAP014A)_GQ900379
	overlap found (494): rep22_1a_repB(pUB110)_X03408
	770 <= 1264
		Scores: 69.91525423728814 cmp 88.01369863013699
Found: rep22_2_repU(pKKS825)_FN377602
Same contig: contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530
	rep22_2_repU(pKKS825)_FN377602 vs repUS12_2_repB(SAP014A)_GQ900379
	overlap found (457): rep22_2_repU(pKKS825)_FN377602
	770 <= 1227
		Scores: 38.40947546531303 cmp 88.01369863013699
Found: repUS40_1_repB(pE394)_KP399637
Saving: contig00038 len=35051 cov=12.9 corr=0 origname=NODE_38_length_35051_cov_12.911408_pilon sw=shovill-spades/1.1.0 date=20240530:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000
Found: rep18b_2_repA(pEF418)_AF408195
Saving: contig00044 len=27996 cov=4.1 corr=10 origname=NODE_44_length_27996_cov_4.112455_pilon sw=shovill-spades/1.1.0 date=20240530:27871..27907:rep18b_2_repA(pEF418)_AF408195:6.560284
Found: rep18b_2_repA(pEF418)_AF408195
Saving: contig00062 len=16064 cov=5.0 corr=6 origname=NODE_62_length_16064_cov_4.979105_pilon sw=shovill-spades/1.1.0 date=20240530:569..608:rep18b_2_repA(pEF418)_AF408195:6.746238
Found: rep18b_2_repA(pEF418)_AF408195
Saving: contig00076 len=11206 cov=4.6 corr=3 origname=NODE_76_length_11206_cov_4.625688_pilon sw=shovill-spades/1.1.0 date=20240530:91..127:rep18b_2_repA(pEF418)_AF408195:6.382979
Found: rep18b_2_repA(pEF418)_AF408195
Saving: contig00100 len=2342 cov=4.7 corr=1 origname=NODE_100_length_2342_cov_4.734086_pilon sw=shovill-spades/1.1.0 date=20240530:2133..2173:rep18b_2_repA(pEF418)_AF408195:7.092199
Found: rep18b_2_repA(pEF418)_AF408195
Saving: contig00111 len=1300 cov=4.2 corr=0 origname=NODE_111_length_1300_cov_4.218244_pilon sw=shovill-spades/1.1.0 date=20240530:1174..1210:rep18b_2_repA(pEF418)_AF408195:6.560284
Found: rep18b_2_repA(pEF418)_AF408195
Same contig: contig00111 len=1300 cov=4.2 corr=0 origname=NODE_111_length_1300_cov_4.218244_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00111 len=1300 cov=4.2 corr=0 origname=NODE_111_length_1300_cov_4.218244_pilon sw=shovill-spades/1.1.0 date=20240530
	rep18b_2_repA(pEF418)_AF408195 vs rep18b_2_repA(pEF418)_AF408195
	ignore overlap (-1048): rep18b_2_repA(pEF418)_AF408195
Saving: contig00111 len=1300 cov=4.2 corr=0 origname=NODE_111_length_1300_cov_4.218244_pilon sw=shovill-spades/1.1.0 date=20240530:90..126:rep18b_2_repA(pEF418)_AF408195:6.560284
Found: rep18b_2_repA(pEF418)_AF408195
Saving: contig00121 len=378 cov=5.8 corr=0 origname=NODE_121_length_378_cov_5.812749_pilon sw=shovill-spades/1.1.0 date=20240530:249..289:rep18b_2_repA(pEF418)_AF408195:7.092199
Found: rep9b_2_prgW(EF62pC)_CP002494
Saving: contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530:17733..18746:rep9b_2_prgW(EF62pC)_CP002494:100.000000
Found: rep9b_1_prgW(pBEE99)_GU046453
Same contig: contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530
	rep9b_1_prgW(pBEE99)_GU046453 vs rep9b_2_prgW(EF62pC)_CP002494
	overlap found (1013): rep9b_1_prgW(pBEE99)_GU046453
Found: rep9b_4_repA2(pTEF2)_AE016831
Same contig: contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530
	rep9b_4_repA2(pTEF2)_AE016831 vs rep9b_2_prgW(EF62pC)_CP002494
	overlap found (956): rep9b_4_repA2(pTEF2)_AE016831
	1013 <= 1969
		Scores: 92.98159121140806 cmp 100.0
Found: rep9b_3_repA(pMG2200)_AB374546
Same contig: contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00016 len=60038 cov=9.4 corr=0 origname=NODE_16_length_60038_cov_9.358382_pilon sw=shovill-spades/1.1.0 date=20240530
	rep9b_3_repA(pMG2200)_AB374546 vs rep9b_2_prgW(EF62pC)_CP002494
	overlap found (942): rep9b_3_repA(pMG2200)_AB374546
	1013 <= 1955
		Scores: 90.4794483118106 cmp 100.0
Found: repUS43_1_CDS12738(DOp1)_CP003584
Saving: contig00075 len=12074 cov=14.1 corr=0 origname=NODE_75_length_12074_cov_14.063531_pilon sw=shovill-spades/1.1.0 date=20240530:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000
Found: rep7a_8_ORF11(pRE25)_X92945
Saving: contig00089 len=5337 cov=4.2 corr=5 origname=NODE_89_length_5337_cov_4.213244_pilon sw=shovill-spades/1.1.0 date=20240530:1123..2061:rep7a_8_ORF11(pRE25)_X92945:100.000000
Found: rep7a_7_rep(pKH7)_NC002096
Same contig: contig00089 len=5337 cov=4.2 corr=5 origname=NODE_89_length_5337_cov_4.213244_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00089 len=5337 cov=4.2 corr=5 origname=NODE_89_length_5337_cov_4.213244_pilon sw=shovill-spades/1.1.0 date=20240530
	rep7a_7_rep(pKH7)_NC002096 vs rep7a_8_ORF11(pRE25)_X92945
	overlap found (864): rep7a_7_rep(pKH7)_NC002096
	938 <= 1802
		Scores: 90.2465166130761 cmp 100.0
Found: rep7a_9_repI(pGB354)_SAU83488
Same contig: contig00089 len=5337 cov=4.2 corr=5 origname=NODE_89_length_5337_cov_4.213244_pilon sw=shovill-spades/1.1.0 date=20240530 == contig00089 len=5337 cov=4.2 corr=5 origname=NODE_89_length_5337_cov_4.213244_pilon sw=shovill-spades/1.1.0 date=20240530
	rep7a_9_repI(pGB354)_SAU83488 vs rep7a_8_ORF11(pRE25)_X92945
	overlap found (595): rep7a_9_repI(pGB354)_SAU83488
	938 <= 1533
		Scores: 99.49804859024323 cmp 100.0
{'plasmidfinder': {'results': {'Enterobacteriales': {'enterobacteriales': 'No '
                                                                          'hit '
                                                                          'found'},
                               'Gram Positive': {'Inc18': 'No hit found',
                                                 'NT_Rep': 'No hit found',
                                                 'Rep1': {'contig00102 len=2082 cov=4.1 corr=0 origname=NODE_102_length_2082_cov_4.148849_pilon sw=shovill-spades/1.1.0 date=20240530:1187..1957:repUS12_2_repB(SAP014A)_GQ900379:88.013699': {'HSP_length': 771,
                                                                                                                                                                                                                                               'accession': 'GQ900379',
                                                                                                                                                                                                                                               'contig_name': 'contig00102 '
                                                                                                                                                                                                                                                              'len=2082 '
                                                                                                                                                                                                                                                              'cov=4.1 '
                                                                                                                                                                                                                                                              'corr=0 '
                                                                                                                                                                                                                                                              'origname=NODE_102_length_2082_cov_4.148849_pilon '
                                                                                                                                                                                                                                                              'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                              'date=20240530',
                                                                                                                                                                                                                                               'coverage': 88.01,
                                                                                                                                                                                                                                               'hit_id': 'contig00102 '
                                                                                                                                                                                                                                                         'len=2082 '
                                                                                                                                                                                                                                                         'cov=4.1 '
                                                                                                                                                                                                                                                         'corr=0 '
                                                                                                                                                                                                                                                         'origname=NODE_102_length_2082_cov_4.148849_pilon '
                                                                                                                                                                                                                                                         'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                         'date=20240530:1187..1957:repUS12_2_repB(SAP014A)_GQ900379:88.013699',
                                                                                                                                                                                                                                               'identity': 100.0,
                                                                                                                                                                                                                                               'note': 'repB(SAP014A)',
                                                                                                                                                                                                                                               'plasmid': 'repUS12',
                                                                                                                                                                                                                                               'position_in_ref': '1..771',
                                                                                                                                                                                                                                               'positions_in_contig': '1187..1957',
                                                                                                                                                                                                                                               'template_length': 876}},
                                                 'Rep2': 'No hit found',
                                                 'Rep3': {'contig00038 len=35051 cov=12.9 corr=0 origname=NODE_38_length_35051_cov_12.911408_pilon sw=shovill-spades/1.1.0 date=20240530:21156..22313:repUS40_1_repB(pE394)_KP399637:100.000000': {'HSP_length': 1158,
                                                                                                                                                                                                                                                   'accession': 'KP399637',
                                                                                                                                                                                                                                                   'contig_name': 'contig00038 '
                                                                                                                                                                                                                                                                  'len=35051 '
                                                                                                                                                                                                                                                                  'cov=12.9 '
                                                                                                                                                                                                                                                                  'corr=0 '
                                                                                                                                                                                                                                                                  'origname=NODE_38_length_35051_cov_12.911408_pilon '
                                                                                                                                                                                                                                                                  'sw=shovill-spades/1.1.0 '
                                                                                                  
..
                                                                                                                                                                                                                                        'len=60038 '
                                                                                                                                                                                                                                                            'cov=9.4 '
                                                                                                                                                                                                                                                            'corr=0 '
                                                                                                                                                                                                                                                            'origname=NODE_16_length_60038_cov_9.358382_pilon '
                                                                                                                                                                                                                                                            'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                            'date=20240530:17733..18746:rep9b_2_prgW(EF62pC)_CP002494:100.000000',
                                                                                                                                                                                                                                                  'identity': 100.0,
                                                                                                                                                                                                                                                  'note': 'prgW(EF62pC)',
                                                                                                                                                                                                                                                  'plasmid': 'rep9b',
                                                                                                                                                                                                                                                  'position_in_ref': '1..1014',
                                                                                                                                                                                                                                                  'positions_in_contig': '17733..18746',
                                                                                                                                                                                                                                                  'template_length': 1014}},
                                                 'RepL': 'No hit found',
                                                 'Rep_trans': {'contig00075 len=12074 cov=14.1 corr=0 origname=NODE_75_length_12074_cov_14.063531_pilon sw=shovill-spades/1.1.0 date=20240530:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000': {'HSP_length': 1206,
                                                                                                                                                                                                                                                         'accession': 'CP003584',
                                                                                                                                                                                                                                                         'contig_name': 'contig00075 '
                                                                                                                                                                                                                                                                        'len=12074 '
                                                                                                                                                                                                                                                                        'cov=14.1 '
                                                                                                                                                                                                                                                                        'corr=0 '
                                                                                                                                                                                                                                                                        'origname=NODE_75_length_12074_cov_14.063531_pilon '
                                                                                                                                                                                                                                                                        'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                                        'date=20240530',
                                                                                                                                                                                                                                                         'coverage': 100.0,
                                                                                                                                                                                                                                                         'hit_id': 'contig00075 '
                                                                                                                                                                                                                                                                   'len=12074 '
                                                                                                                                                                                                                                                                   'cov=14.1 '
                                                                                                                                                                                                                                                                   'corr=0 '
                                                                                                                                                                                                                                                                   'origname=NODE_75_length_12074_cov_14.063531_pilon '
                                                                                                                                                                                                                                                                   'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                                   'date=20240530:8225..9430:repUS43_1_CDS12738(DOp1)_CP003584:100.000000',
                                                                                                                                                                                                                                                         'identity': 100.0,
                                                                                                                                                                                                                                                         'note': 'CDS12738(DOp1)',
                                                                                                                                                                                                                                                         'plasmid': 'repUS43',
                                                                                                                                                                                                                                                         'position_in_ref': '1..1206',
                                                                                                                                                                                                                                                         'positions_in_contig': '8225..9430',
                                                                                                                                                                                                                                                         'template_length': 1206},
                                                               'contig00089 len=5337 cov=4.2 corr=5 origname=NODE_89_length_5337_cov_4.213244_pilon sw=shovill-spades/1.1.0 date=20240530:1123..2061:rep7a_8_ORF11(pRE25)_X92945:100.000000': {'HSP_length': 939,
                                                                                                                                                                                                                                               'accession': 'X92945',
                                                                                                                                                                                                                                               'contig_name': 'contig00089 '
                                                                                                                                                                                                                                                              'len=5337 '
                                                                                                                                                                                                                                                              'cov=4.2 '
                                                                                                                                                                                                                                                              'corr=5 '
                                                                                                                                                                                                                                                              'origname=NODE_89_length_5337_cov_4.213244_pilon '
                                                                                                                                                                                                                                                              'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                              'date=20240530',
                                                                                                                                                                                                                                               'coverage': 100.0,
                                                                                                                                                                                                                                               'hit_id': 'contig00089 '
                                                                                                                                                                                                                                                         'len=5337 '
                                                                                                                                                                                                                                                         'cov=4.2 '
                                                                                                                                                                                                                                                         'corr=5 '
                                                                                                                                                                                                                                                         'origname=NODE_89_length_5337_cov_4.213244_pilon '
                                                                                                                                                                                                                                                         'sw=shovill-spades/1.1.0 '
                                                                                                                                                                                                                                                         'date=20240530:1123..2061:rep7a_8_ORF11(pRE25)_X92945:100.000000',
                                                                                                                                                                                                                                               'identity': 100.0,
                                                                                                                                                                                                                                               'note': 'ORF11(pRE25)',
                                                                                                                                                                                                                                               'plasmid': 'rep7a',
                                                                                                                                                                                                                                               'position_in_ref': '1..939',
                                                                                                                                                                                                                                               'positions_in_contig': '1123..2061',
                                                                                                                                                                                                                                               'template_length': 939}}}},
                   'run_info': {'date': '07.10.2025', 'time': '15:41:34'},
                   'user_input': {'file_format': 'fasta',
                                  'filename(s)': ['/tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat'],
                                  'method': 'blast'}}}

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e6c3eaaaa39311f0a35e0022480b3a6c"

              

              
chromInfo
"/tmp/tmpxt_eqome/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input
{"database_name": "plasmidfinder_81c11f4_2023_12_04", "input_file": {"values": [{"id": 1, "src": "hda"}]}}

              

              
options
{"min_cov": "0.6", "threshold": "0.95"}

              

              
output_files
{"output_selection": ["hit_fasta", "plasmid_fasta", "result_tsv", "result_txt", "data_json"]}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 8: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              mkdir -p ./database_path/amrfinderplus-db && ln -s '/cvmfs/data.galaxyproject.org/byhand/bakta_database/7669534'/* database_path && ln -s '/cvmfs/data.galaxyproject.org/byhand/amrfinderplus-db/amrfinderplus_V3.12_2024-05-02.2/' database_path/amrfinderplus-db/latest &&  bakta --verbose --threads ${GALAXY_SLOTS:-1} --db './database_path' --output 'bakta_output' --min-contig-length 1 --prefix bakta_output  --translation-table '11' --gram '?'     '/tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat' | tee 'XXXX'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              Bakta v1.9.4
Options and arguments:
	input: /tmp/tmpxt_eqome/files/2/6/c/dataset_26cfc52f-fa89-48b1-b4a9-f515e51292e3.dat
	db: /tmp/tmpxt_eqome/job_working_directory/000/5/working/database_path, version 5.0, full
	output: /tmp/tmpxt_eqome/job_working_directory/000/5/working/bakta_output
	tmp directory: /tmp/tmpxt_eqome/job_working_directory/000/5/tmp/tmp35p6qxxj
	prefix: bakta_output
	threads: 1
	translation table: 11

parse genome sequences...
	imported: 153
	filtered & revised: 153
	contigs: 153

start annotation...
predict tRNAs...
	found: 60
predict tmRNAs...
	found: 1
predict rRNAs...
	found: 6
predict ncRNAs...
	found: 36
predict ncRNA regions...
	found: 43
predict CRISPR arrays...
	found: 1
predict & annotate CDSs...
	predicted: 2886 
	discarded spurious: 0
	revised translational exceptions: 0
	detected IPSs: 2621
	found PSCs: 205
	found PSCCs: 30
	lookup annotations...
	conduct expert systems...
		amrfinder: 12
		protein sequences: 44
	combine annotations and mark hypotheticals...
	detect pseudogenes...
		pseudogene candidates: 19
		found pseudogenes: 10
analyze hypothetical proteins: 36
	detected Pfam hits: 7 
	calculated proteins statistics
	revise special cases...
extract sORF...
	potential: 42490
	discarded due to overlaps: 35967
	discarded spurious: 0
	detected IPSs: 11
	found PSCs: 0
	lookup annotations...
	filter and combine annotations...
	filtered sORFs: 5
detect gaps...
	found: 0
detect oriCs/oriVs...
	found: 4
detect oriTs...
	found: 0
apply feature overlap filters...
select features and create locus tags...
selected: 3040
improve annotations...
	revised gene symbols: 21

genome statistics:
	Genome size: 3,027,467 bp
	Contigs/replicons: 153
	GC: 37.3 %
	N50: 44,557
	N ratio: 0.0 %
	coding density: 86.7 %

annotation summary:
	tRNAs: 59
	tmRNAs: 1
	rRNAs: 6
	ncRNAs: 36
	ncRNA regions: 43
	CRISPR arrays: 1
	CDSs: 2886
		hypotheticals: 36
		pseudogenes: 10
		signal peptides: 0
	sORFs: 4
	gaps: 0
	oriCs/oriVs: 4
	oriTs: 0

export annotation results to: /tmp/tmpxt_eqome/job_working_directory/000/5/working/bakta_output
	human readable TSV...
	GFF3...
	INSDC GenBank & EMBL...
	genome sequences...
	feature nucleotide sequences...
	translated CDS sequences...
	circular genome plot...
	hypothetical TSV...
	translated hypothetical CDS sequences...
	machine readable JSON...
	genome and annotation summary...

If you use these results please cite Bakta: https://doi.org/10.1099/mgen.0.000685
Annotation successfully finished in 76:50 [mm:ss].

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e6c3eaaaa39311f0a35e0022480b3a6c"

              

              
annotation
{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}

              

              
chromInfo
"/tmp/tmpxt_eqome/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_option
{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.0_2023-02-20", "input_file": {"values": [{"id": 1, "src": "hda"}]}, "min_contig_length": null}

              

              
organism
{"genus": null, "plasmid": null, "species": null, "strain": null}

              

              
output_files
{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "file_gbff", "file_embl", "file_fna", "file_faa", "hypo_tsv", "hypo_fa", "file_json", "sum_txt"]}

              

              
workflow
{"skip_analysis": null}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 9: ToolDistillator:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator plasmidfinder --hid '12' '/tmp/tmpxt_eqome/files/1/2/4/dataset_1245602f-5fa0-430e-97a5-840bf17e1c1b.dat' --analysis_software_version '2.1.6+galaxy1' --reference_database_version 'plasmidfinder_81c11f4_2023_12_04' --plasmid_result_tabular_path '/tmp/tmpxt_eqome/files/8/2/1/dataset_82166226-1e66-4d23-a9c2-fdec296c0ec6.dat' --plasmid_result_tabular_hid '15' --genome_hit_path '/tmp/tmpxt_eqome/files/e/4/3/dataset_e43488db-8914-44d5-ba1e-7d20d4ab1c9a.dat' --genome_hit_hid '13' --plasmid_hit_path '/tmp/tmpxt_eqome/files/1/b/c/dataset_1bc3c4d2-ce21-43c4-87bb-6b4be732ff56.dat' --plasmid_hit_hid '14' -o 'tooldistillator_folder/plasmidfinder_0_output.json' | tee 'XXXX' &&  tooldistillator isescan --hid '4' '/tmp/tmpxt_eqome/files/8/8/2/dataset_88292597-67f6-437d-a53a-ff38db79e4c0.dat' --analysis_software_version '1.7.3+galaxy0' --reference_database_version '' --summary_path '/tmp/tmpxt_eqome/files/6/c/5/dataset_6c52b267-88dc-4e7d-8e6e-f29435afefa5.dat' --summary_hid '3' --annotation_path '/tmp/tmpxt_eqome/files/8/1/8/dataset_818cc123-d635-4a2b-b096-cc70a4e9a887.dat' --annotation_hid '5' --orf_fna_path '/tmp/tmpxt_eqome/files/0/d/3/dataset_0d3f6ad5-0b63-4761-8023-230bdbe13e85.dat' --orf_fna_hid '7' --orf_faa_path '/tmp/tmpxt_eqome/files/0/f/b/dataset_0fb8f44f-768d-484d-86df-4107777645b8.dat' --orf_faa_hid '8' --is_fna_path '/tmp/tmpxt_eqome/files/6/4/2/dataset_642cdce2-8b31-4f1c-8842-1fcfb43cf988.dat' --is_fna_hid '6' -o 'tooldistillator_folder/isescan_1_output.json' | tee 'XXXX' &&  tooldistillator integronfinder2 --hid '10' '/tmp/tmpxt_eqome/files/e/d/9/dataset_ed99dd81-3907-47a4-a603-9e6471e7d946.dat' --analysis_software_version '2.0.5+galaxy0' --reference_database_version '' --summary_file_path '/tmp/tmpxt_eqome/files/6/b/9/dataset_6b9aff41-638a-43f0-8286-2fa0729b8be8.dat' --summary_file_hid '11' -o 'tooldistillator_folder/integronfinder2_2_output.json' | tee 'XXXX' &&  tooldistillator bakta --hid '27' '/tmp/tmpxt_eqome/files/1/d/4/dataset_1d494725-deaa-43e9-a4bb-1f3ec028815e.dat' --analysis_software_version '1.9.4+galaxy1' --reference_database_version 'V5.0_2023-02-20' --annotation_tabular_path '/tmp/tmpxt_eqome/files/c/b/e/dataset_cbe1ea91-74a2-4a92-9e71-3d57756b0ca9.dat' --annotation_tabular_hid '17' --annotation_genbank_path '/tmp/tmpxt_eqome/files/a/f/9/dataset_af922765-0e1e-4290-9b08-96c60fb398b4.dat' --annotation_genbank_hid '19' --annotation_embl_path '/tmp/tmpxt_eqome/files/f/0/1/dataset_f0126e80-44fb-45a5-a9a3-1f7aa2776858.dat' --annotation_embl_hid '20' --contig_sequences_path '/tmp/tmpxt_eqome/files/2/8/4/dataset_284f03b2-f228-4698-853a-60b1b4d6b417.dat' --contig_sequences_hid '21' --nucleotide_annotation_path '/tmp/tmpxt_eqome/files/c/f/5/dataset_cf5d7c9c-4b01-49be-afcf-9bc7d71cccef.dat' --nucleotide_annotation_hid '22' --amino_acid_annotation_path '/tmp/tmpxt_eqome/files/0/8/c/dataset_08cd1786-6a8a-4811-bbf4-25e57386ec3f.dat' --amino_acid_annotation_hid '23' --summary_result_path '/tmp/tmpxt_eqome/files/5/0/1/dataset_5014cdb3-af39-43ce-896b-66dd3ab7e518.dat' --summary_result_hid '26' --gff_file_path '/tmp/tmpxt_eqome/files/c/a/8/dataset_ca82b640-b837-4aca-bf58-bb2ebe705814.dat' --gff_file_hid '18' --hypothetical_protein_path '/tmp/tmpxt_eqome/files/9/c/f/dataset_9cfc2af5-fb32-4f65-b9e3-6076165a7e3e.dat' --hypothetical_protein_hid '25' --hypothetical_tabular_path '/tmp/tmpxt_eqome/files/8/5/6/dataset_85671993-54ab-4de1-b4a1-b8224ba2373b.dat' --hypothetical_tabular_hid '24' --plot_file_path '/tmp/tmpxt_eqome/files/6/b/0/dataset_6b09e856-fb48-4426-95b7-8c68f8f4c197.dat' --plot_file_hid '28' -o 'tooldistillator_folder/bakta_3_output.json' | tee 'XXXX'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              + mkdir tooldistillator_folder
+ tooldistillator plasmidfinder --hid 12 /tmp/tmpxt_eqome/files/1/2/4/dataset_1245602f-5fa0-430e-97a5-840bf17e1c1b.dat --analysis_software_version 2.1.6+galaxy1 --reference_database_version plasmidfinder_81c11f4_2023_12_04 --plasmid_result_tabular_path /tmp/tmpxt_eqome/files/8/2/1/dataset_82166226-1e66-4d23-a9c2-fdec296c0ec6.dat --plasmid_result_tabular_hid 15 --genome_hit_path /tmp/tmpxt_eqome/files/e/4/3/dataset_e43488db-8914-44d5-ba1e-7d20d4ab1c9a.dat --genome_hit_hid 13 --plasmid_hit_path /tmp/tmpxt_eqome/files/1/b/c/dataset_1bc3c4d2-ce21-43c4-87bb-6b4be732ff56.dat --plasmid_hit_hid 14 -o tooldistillator_folder/plasmidfinder_0_output.json
+ tee XXXX
10/07/2025 04:59:32 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/1/2/4/dataset_1245602f-5fa0-430e-97a5-840bf17e1c1b.dat
10/07/2025 04:59:32 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/e/4/3/dataset_e43488db-8914-44d5-ba1e-7d20d4ab1c9a.dat
10/07/2025 04:59:32 PM: plasmidfinderio.py: Analysis of genome_hit_path
10/07/2025 04:59:32 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/1/b/c/dataset_1bc3c4d2-ce21-43c4-87bb-6b4be732ff56.dat
10/07/2025 04:59:32 PM: plasmidfinderio.py: Analysis of plasmid_hit_path
+ tooldistillator isescan --hid 4 /tmp/tmpxt_eqome/files/8/8/2/dataset_88292597-67f6-437d-a53a-ff38db79e4c0.dat --analysis_software_version 1.7.3+galaxy0 --reference_database_version '' --summary_path /tmp/tmpxt_eqome/files/6/c/5/dataset_6c52b267-88dc-4e7d-8e6e-f29435afefa5.dat --summary_hid 3 --annotation_path /tmp/tmpxt_eqome/files/8/1/8/dataset_818cc123-d635-4a2b-b096-cc70a4e9a887.dat --annotation_hid 5 --orf_fna_path /tmp/tmpxt_eqome/files/0/d/3/dataset_0d3f6ad5-0b63-4761-8023-230bdbe13e85.dat --orf_fna_hid 7 --orf_faa_path /tmp/tmpxt_eqome/files/0/f/b/dataset_0fb8f44f-768d-484d-86df-4107777645b8.dat --orf_faa_hid 8 --is_fna_path /tmp/tmpxt_eqome/files/6/4/2/dataset_642cdce2-8b31-4f1c-8842-1fcfb43cf988.dat --is_fna_hid 6 -o tooldistillator_folder/isescan_1_output.json
+ tee XXXX
10/07/2025 04:59:34 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/8/8/2/dataset_88292597-67f6-437d-a53a-ff38db79e4c0.dat
10/07/2025 04:59:34 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/0/d/3/dataset_0d3f6ad5-0b63-4761-8023-230bdbe13e85.dat
10/07/2025 04:59:34 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/0/f/b/dataset_0fb8f44f-768d-484d-86df-4107777645b8.dat
10/07/2025 04:59:34 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/6/4/2/dataset_642cdce2-8b31-4f1c-8842-1fcfb43cf988.dat
10/07/2025 04:59:34 PM: interfaces.py: Extraction of: summary_path
10/07/2025 04:59:34 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/6/c/5/dataset_6c52b267-88dc-4e7d-8e6e-f29435afefa5.dat
10/07/2025 04:59:34 PM: interfaces.py: Extraction of: annotation_path
10/07/2025 04:59:34 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/8/1/8/dataset_818cc123-d635-4a2b-b096-cc70a4e9a887.dat
+ tooldistillator integronfinder2 --hid 10 /tmp/tmpxt_eqome/files/e/d/9/dataset_ed99dd81-3907-47a4-a603-9e6471e7d946.dat --analysis_software_version 2.0.5+galaxy0 --reference_database_version '' --summary_file_path /tmp/tmpxt_eqome/files/6/b/9/dataset_6b9aff41-638a-43f0-8286-2fa0729b8be8.dat --summary_file_hid 11 -o tooldistillator_folder/integronfinder2_2_output.json
+ tee XXXX
10/07/2025 04:59:35 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/e/d/9/dataset_ed99dd81-3907-47a4-a603-9e6471e7d946.dat
/usr/local/lib/python3.13/site-packages/tooldistillator/toolsio/integronfinder2io.py:48: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
  integron_df.fillna("", inplace=True)
10/07/2025 04:59:35 PM: integronfinder2io.py: Analysis of summary_file_path
10/07/2025 04:59:35 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/6/b/9/dataset_6b9aff41-638a-43f0-8286-2fa0729b8be8.dat
+ tooldistillator bakta --hid 27 /tmp/tmpxt_eqome/files/1/d/4/dataset_1d494725-deaa-43e9-a4bb-1f3ec028815e.dat --analysis_software_version 1.9.4+galaxy1 --reference_database_version V5.0_2023-02-20 --annotation_tabular_path /tmp/tmpxt_eqome/files/c/b/e/dataset_cbe1ea91-74a2-4a92-9e71-3d57756b0ca9.dat --annotation_tabular_hid 17 --annotation_genbank_path /tmp/tmpxt_eqome/files/a/f/9/dataset_af922765-0e1e-4290-9b08-96c60fb398b4.dat --annotation_genbank_hid 19 --annotation_embl_path /tmp/tmpxt_eqome/files/f/0/1/dataset_f0126e80-44fb-45a5-a9a3-1f7aa2776858.dat --annotation_embl_hid 20 --contig_sequences_path /tmp/tmpxt_eqome/files/2/8/4/dataset_284f03b2-f228-4698-853a-60b1b4d6b417.dat --contig_sequences_hid 21 --nucleotide_annotation_path /tmp/tmpxt_eqome/files/c/f/5/dataset_cf5d7c9c-4b01-49be-afcf-9bc7d71cccef.dat --nucleotide_annotation_hid 22 --amino_acid_annotation_path /tmp/tmpxt_eqome/files/0/8/c/dataset_08cd1786-6a8a-4811-bbf4-25e57386ec3f.dat --amino_acid_annotation_hid 23 --summary_result_path /tmp/tmpxt_eqome/files/5/0/1/dataset_5014cdb3-af39-43ce-896b-66dd3ab7e518.dat --summary_result_hid 26 --gff_file_path /tmp/tmpxt_eqome/files/c/a/8/dataset_ca82b640-b837-4aca-bf58-bb2ebe705814.dat --gff_file_hid 18 --hypothetical_protein_path /tmp/tmpxt_eqome/files/9/c/f/dataset_9cfc2af5-fb32-4f65-b9e3-6076165a7e3e.dat --hypothetical_protein_hid 25 --hypothetical_tabular_path /tmp/tmpxt_eqome/files/8/5/6/dataset_85671993-54ab-4de1-b4a1-b8224ba2373b.dat --hypothetical_tabular_hid 24 --plot_file_path /tmp/tmpxt_eqome/files/6/b/0/dataset_6b09e856-fb48-4426-95b7-8c68f8f4c197.dat --plot_file_hid 28 -o tooldistillator_folder/bakta_3_output.json
+ tee XXXX
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/1/d/4/dataset_1d494725-deaa-43e9-a4bb-1f3ec028815e.dat
10/07/2025 04:59:37 PM: baktaio.py: bakta input file imported
10/07/2025 04:59:37 PM: baktaio.py: summary_result_path analysis
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/5/0/1/dataset_5014cdb3-af39-43ce-896b-66dd3ab7e518.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: annotation_tabular_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/c/b/e/dataset_cbe1ea91-74a2-4a92-9e71-3d57756b0ca9.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: gff_file_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/c/a/8/dataset_ca82b640-b837-4aca-bf58-bb2ebe705814.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: annotation_genbank_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/a/f/9/dataset_af922765-0e1e-4290-9b08-96c60fb398b4.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: annotation_embl_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/f/0/1/dataset_f0126e80-44fb-45a5-a9a3-1f7aa2776858.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: contig_sequences_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/2/8/4/dataset_284f03b2-f228-4698-853a-60b1b4d6b417.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: nucleotide_annotation_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/c/f/5/dataset_cf5d7c9c-4b01-49be-afcf-9bc7d71cccef.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: amino_acid_annotation_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/0/8/c/dataset_08cd1786-6a8a-4811-bbf4-25e57386ec3f.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: hypothetical_protein_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/9/c/f/dataset_9cfc2af5-fb32-4f65-b9e3-6076165a7e3e.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: hypothetical_tabular_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/8/5/6/dataset_85671993-54ab-4de1-b4a1-b8224ba2373b.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: summary_result_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/5/0/1/dataset_5014cdb3-af39-43ce-896b-66dd3ab7e518.dat
10/07/2025 04:59:37 PM: interfaces.py: Extraction of: plot_file_path
10/07/2025 04:59:37 PM: interfaces.py: Treatment of /tmp/tmpxt_eqome/files/6/b/0/dataset_6b09e856-fb48-4426-95b7-8c68f8f4c197.dat

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e6c3eaaaa39311f0a35e0022480b3a6c"

              

              
chromInfo
"/tmp/tmpxt_eqome/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
log
false

              

              
tool_section
{"tools": [{"__index__": 0, "select_tool": {"__current_case__": 30, "genome_hit_path": {"values": [{"id": 13, "src": "hda"}]}, "input": {"values": [{"id": 12, "src": "hda"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "plasmid_hit_path": {"values": [{"id": 14, "src": "hda"}]}, "plasmid_result_tabular_path": {"values": [{"id": 15, "src": "hda"}]}, "reference_database_version": "plasmidfinder_81c11f4_2023_12_04", "tool_list": "plasmidfinder"}}, {"__index__": 1, "select_tool": {"__current_case__": 22, "annotation_path": {"values": [{"id": 5, "src": "hda"}]}, "input": {"values": [{"id": 4, "src": "hda"}]}, "is_fna_path": {"values": [{"id": 6, "src": "hda"}]}, "orf_faa_path": {"values": [{"id": 8, "src": "hda"}]}, "orf_fna_path": {"values": [{"id": 7, "src": "hda"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "summary_path": {"values": [{"id": 3, "src": "hda"}]}, "tool_list": "isescan"}}, {"__index__": 2, "select_tool": {"__current_case__": 21, "input": {"values": [{"id": 10, "src": "hda"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "summary_file_path": {"values": [{"id": 11, "src": "hda"}]}, "tool_list": "integronfinder2"}}, {"__index__": 3, "select_tool": {"__current_case__": 3, "amino_acid_annotation_path": {"values": [{"id": 23, "src": "hda"}]}, "annotation_embl_path": {"values": [{"id": 20, "src": "hda"}]}, "annotation_genbank_path": {"values": [{"id": 19, "src": "hda"}]}, "annotation_tabular_path": {"values": [{"id": 17, "src": "hda"}]}, "contig_sequences_path": {"values": [{"id": 21, "src": "hda"}]}, "gff_file_path": {"values": [{"id": 18, "src": "hda"}]}, "hypothetical_protein_path": {"values": [{"id": 25, "src": "hda"}]}, "hypothetical_tabular_path": {"values": [{"id": 24, "src": "hda"}]}, "input": {"values": [{"id": 27, "src": "hda"}]}, "nucleotide_annotation_path": {"values": [{"id": 22, "src": "hda"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "plot_file_path": {"values": [{"id": 28, "src": "hda"}]}, "reference_database_version": "V5.0_2023-02-20", "summary_result_path": {"values": [{"id": 26, "src": "hda"}]}, "tool_list": "bakta"}}]}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 10: ToolDistillator summarize:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              tooldistillator --version && mkdir -p input_files && cp '/tmp/tmpxt_eqome/files/4/e/b/dataset_4eb48cfd-47e2-4423-a94b-61bda02f8afa.dat' ./input_files/ && cp '/tmp/tmpxt_eqome/files/1/8/f/dataset_18f79470-cb53-4d21-9e00-24acd3feed81.dat' ./input_files/ && cp '/tmp/tmpxt_eqome/files/0/3/6/dataset_0367f87d-bed6-44e1-b414-2824a207fde4.dat' ./input_files/ && cp '/tmp/tmpxt_eqome/files/1/a/7/dataset_1a76afa7-a776-4926-a389-b9075626ece7.dat' ./input_files/ && tooldistillator summarize input_files/* -o summary.json
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              tooldistillator 1.0.1

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e6c3eaaaa39311f0a35e0022480b3a6c"

              

              
chromInfo
"/tmp/tmpxt_eqome/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        history_id
        

          

        • 85707c376c908dc1
          • 

        

        • 

      • 

        history_state
        

          

        • ok
          • 

        

        • 

      • 

        invocation_id
        

          

        • 85707c376c908dc1
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • 85707c376c908dc1
          • 

        

        • 

      

      

      • 

    
  
    

    • 





      		
    

  





        


            

            
            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    
















  
  

    

      

  




      


    


    

      

        
      

  
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