Update bacterial_genome_annotation WF by SantaMcCloud · Pull Request #1099 · galaxyproject/iwc

SantaMcCloud · 2026-02-07T20:32:34Z

FOR CONTRIBUTOR:

I have read the Adding workflows guidelines
License permits unrestricted use (educational + commercial)
Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

.dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
Changelog contains appropriate entries
Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

SantaMcCloud · 2026-02-07T20:38:57Z

I made some modifications to your workflow, which still keep the original work. The only little changes i did are that Tooldistillator is now optional to run, and that some Bakta outputs are formatted and put together. These changes are made because we would like to use your WF in a different WF. @paulzierep or @bebatut can give you more details to this if there are any question!

github-actions · 2026-02-07T20:47:41Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ bacterial_genome_annotation.ga_0
Execution Problem:
- 'identifier'

github-actions · 2026-02-07T21:25:41Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ bacterial_genome_annotation.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 12 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Plasmid detection database:
- step_state: scheduled
Step 2: Bacterial genome annotation database:
- step_state: scheduled
Step 3: AMRFinderPlus database:
- step_state: scheduled
Step 4: Run ToolDistillator without bakta:
- step_state: scheduled
Step 5: Run ToolDistillator with only bakta:
- step_state: scheduled
Step 6: Run Bakta:
- step_state: scheduled
Step 7: Sequence collection:
- step_state: scheduled

Step 8: PlasmidFinder for plasmid detection (toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output_dir && mkdir temp_dir && plasmidfinder.py -i '/tmp/tmpc8o2fawf/files/4/c/e/dataset_4ce81a2e-61f8-45a3-a938-b88a77a9f795.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 Error:

/tmp/tmpc8o2fawf/job_working_directory/000/2/tool_script.sh: line 10: plasmidfinder.py: command not found

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e2ed766046811f18951000d3ad47ab2"`
chromInfo	`"/tmp/tmpc8o2fawf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"database_name": "plasmidfinder_81c11f4_2023_12_04", "input_file": {"values": [{"id": 1, "src": "dce"}]}}`
options	`{"min_cov": "0.6", "threshold": "0.95"}`
output_files	`{"output_selection": ["hit_fasta", "plasmid_fasta", "result_tsv", "result_txt", "data_json"]}`

Step 9: ISEScan for insertion sequence elements detection (toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/isescan:1.7.3--h7b50bb2_0

Command Line:

ln -s '/tmp/tmpc8o2fawf/files/4/c/e/dataset_4ce81a2e-61f8-45a3-a938-b88a77a9f795.dat' input && isescan.py --seqfile input --output 'results'  --nthread ${GALAXY_SLOTS:-7}  | tee '/tmp/tmpc8o2fawf/job_working_directory/000/3/outputs/dataset_9ce27b16-5897-4183-9f74-94a583c47870.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) = 2.3 sec
Time elapsed: 0 hours 0 minutes and 2 seconds.
ISEScan starts at Sat Feb  7 21:03:35 2026
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. Sat Feb  7 21:03:37 2026

Begin to phmmer search against proteome database. Sat Feb  7 21:03:37 2026
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. Sat Feb  7 21:14:17 2026

Begin to profile HMM search against proteome database. Sat Feb  7 21:14:17 2026
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. Sat Feb  7 21:24:07 2026
pred begins at Sat Feb  7 21:24:07 2026
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 Sat Feb  7 21:24:11 2026
Finish addNonORFcopy at Sat Feb  7 21:24:11 2026
Begin addNonORFcopy1 at Sat Feb  7 21:24:15 2026
Finish addNonORFcopy1 at Sat Feb  7 21:24:15 2026
getFullIS() begins at Sat Feb  7 21:24:15 2026
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 Sat Feb  7 21:24:15 2026
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 Sat Feb  7 21:24:15 2026
Begin reading protein database at Sat Feb  7 21:24:15 2026
Finish reading protein database at Sat Feb  7 21:24:15 2026
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 Sat Feb  7 21:24:16 2026
Both complete and partial IS elements are reported.
ISEScan ends at Sat Feb  7 21:24:16 2026

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e2ed766046811f18951000d3ad47ab2"`
chromInfo	`"/tmp/tmpc8o2fawf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
log_activate	`true`
remove_short_is	`false`

Step 10: Integron Finder for integrons detection (toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

integron_finder '/tmp/tmpc8o2fawf/files/4/c/e/dataset_4ce81a2e-61f8-45a3-a938-b88a77a9f795.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:

```
127
```

Standard Error:

/tmp/tmpc8o2fawf/job_working_directory/000/4/tool_script.sh: line 10: integron_finder: command not found

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e2ed766046811f18951000d3ad47ab2"`
chromInfo	`"/tmp/tmpc8o2fawf/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 11: Bakta functionnal annotation (toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is running

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/tmpc8o2fawf/files/4/c/e/dataset_4ce81a2e-61f8-45a3-a938-b88a77a9f795.dat' | tee 'XXXX'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e2ed766046811f18951000d3ad47ab2"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmpc8o2fawf/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": "dce"}]}, "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 12: ToolDistillator without bakta:
- step_state: new
Step 13: Format Bakta output:
- step_state: new
Step 14: Pick the main bakta file if the tool is run.:
- step_state: new

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3e2ed766046811f18951000d3ad47ab2"`
chromInfo	`"/tmp/tmpc8o2fawf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 35, "input": {"values": [{"id": 26, "src": "hdca"}]}, "software": "bakta"}}]`
title	`""`

Step 16: ToolDistillator summarize without bakta:
- step_state: new
Step 17: Merge Bakta Output:
- step_state: new
Step 18: ToolDistillator bakta:
- step_state: new
Step 19: ToolDistillator summarize bakta:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - af698db03d5e9e67
- history_state
  - running
- invocation_id
  - af698db03d5e9e67
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': 'd5794c95ee5f2974', 'reason': 'dataset_failed', 'workflow_step_id': 11}]
- workflow_id
  - af698db03d5e9e67

github-actions · 2026-02-07T21:36:15Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ bacterial_genome_annotation.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 12 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Plasmid detection database:
- step_state: scheduled
Step 2: Bacterial genome annotation database:
- step_state: scheduled
Step 3: AMRFinderPlus database:
- step_state: scheduled
Step 4: Run ToolDistillator without bakta:
- step_state: scheduled
Step 5: Run ToolDistillator with only bakta:
- step_state: scheduled
Step 6: Run Bakta:
- step_state: scheduled
Step 7: Sequence collection:
- step_state: scheduled

Step 8: PlasmidFinder for plasmid detection (toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/plasmidfinder:2.1.6--py314hdfd78af_2

Command Line:

mkdir output_dir && mkdir temp_dir && plasmidfinder.py -i '/tmp/tmp9wx2gg4e/files/e/f/4/dataset_ef4ec6a6-22f4-4c46-af77-dccc81dd0be1.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 Error:

/usr/local/bin/plasmidfinder.py:351: DeprecationWarning: Use shutil.which instead of find_executable
  if find_executable(method_path) is None:

Standard Output:

{'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 '
                                                                                                                                                                                                                                                                  'date=20240530',
                                                                                                                                                                                                                                                   'coverage': 100.0,
                                                                                                                                                                                                                                                   'hit_id': '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',
                                                                                                                                                                                                                                                   'identity': 100.0,
                                                                                                                                                                                                                                                   'note': 'repB(pE394)',
                                                                                                                                                                                                                                                   'plasmid': 'repUS40',
                                                                                                                                                                                                                                                   'position_in_ref': '1..1158',
                                                                                                                                                                                                                                                   'positions_in_contig': '21156..22313',
                                                                                                                                                                                                                                                   'template_length': 1158}},
                                                 'RepA_N': {'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': {'HSP_length': 1014,
                                                                                                                                                                                                                                                  'accession': 'CP002494',
                                                                                                                                                                                                                                                  'contig_name': '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',
                                                                                                                                                                                                                                                  'coverage': 100.0,
                                                                                                                                                                                                                                                  'hit_id': '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',
                                                                                                                                                                                                                                                  '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': '07.02.2026', 'time': '21:13:57'},
                   'user_input': {'file_format': 'fasta',
                                  'filename(s)': ['/tmp/tmp9wx2gg4e/files/e/f/4/dataset_ef4ec6a6-22f4-4c46-af77-dccc81dd0be1.dat'],
                                  'method': 'blast'}}}

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c58ee2ae046911f18951000d3a011c65"`
chromInfo	`"/tmp/tmp9wx2gg4e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"database_name": "plasmidfinder_81c11f4_2023_12_04", "input_file": {"values": [{"id": 1, "src": "dce"}]}}`
options	`{"min_cov": "0.6", "threshold": "0.95"}`
output_files	`{"output_selection": ["hit_fasta", "plasmid_fasta", "result_tsv", "result_txt", "data_json"]}`

Step 9: ISEScan for insertion sequence elements detection (toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/isescan:1.7.3--h7b50bb2_0

Command Line:

ln -s '/tmp/tmp9wx2gg4e/files/e/f/4/dataset_ef4ec6a6-22f4-4c46-af77-dccc81dd0be1.dat' input && isescan.py --seqfile input --output 'results'  --nthread ${GALAXY_SLOTS:-7}  | tee '/tmp/tmp9wx2gg4e/job_working_directory/000/3/outputs/dataset_c3a6db85-2e33-4b24-aa56-dcdc478aae73.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) = 2.8 sec
Time elapsed: 0 hours 0 minutes and 3 seconds.
ISEScan starts at Sat Feb  7 21:13:53 2026
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. Sat Feb  7 21:13:56 2026

Begin to phmmer search against proteome database. Sat Feb  7 21:13:56 2026
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. Sat Feb  7 21:24:29 2026

Begin to profile HMM search against proteome database. Sat Feb  7 21:24:29 2026
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. Sat Feb  7 21:34:19 2026
pred begins at Sat Feb  7 21:34:19 2026
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 Sat Feb  7 21:34:23 2026
Finish addNonORFcopy at Sat Feb  7 21:34:23 2026
Begin addNonORFcopy1 at Sat Feb  7 21:34:27 2026
Finish addNonORFcopy1 at Sat Feb  7 21:34:27 2026
getFullIS() begins at Sat Feb  7 21:34:27 2026
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 Sat Feb  7 21:34:27 2026
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 Sat Feb  7 21:34:27 2026
Begin reading protein database at Sat Feb  7 21:34:27 2026
Finish reading protein database at Sat Feb  7 21:34:27 2026
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 Sat Feb  7 21:34:27 2026
Both complete and partial IS elements are reported.
ISEScan ends at Sat Feb  7 21:34:28 2026

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c58ee2ae046911f18951000d3a011c65"`
chromInfo	`"/tmp/tmp9wx2gg4e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
log_activate	`true`
remove_short_is	`false`

Step 10: Integron Finder for integrons detection (toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

integron_finder '/tmp/tmp9wx2gg4e/files/e/f/4/dataset_ef4ec6a6-22f4-4c46-af77-dccc81dd0be1.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:

```
127
```

Standard Error:

/tmp/tmp9wx2gg4e/job_working_directory/000/4/tool_script.sh: line 10: integron_finder: command not found

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c58ee2ae046911f18951000d3a011c65"`
chromInfo	`"/tmp/tmp9wx2gg4e/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 11: Bakta functionnal annotation (toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is running

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/tmp9wx2gg4e/files/e/f/4/dataset_ef4ec6a6-22f4-4c46-af77-dccc81dd0be1.dat' | tee 'XXXX'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c58ee2ae046911f18951000d3a011c65"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmp9wx2gg4e/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": "dce"}]}, "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 12: ToolDistillator without bakta:
- step_state: new
Step 13: Format Bakta output:
- step_state: new
Step 14: Pick the main bakta file if the tool is run.:
- step_state: new

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c58ee2ae046911f18951000d3a011c65"`
chromInfo	`"/tmp/tmp9wx2gg4e/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 35, "input": {"values": [{"id": 26, "src": "hdca"}]}, "software": "bakta"}}]`
title	`""`

Step 16: ToolDistillator summarize without bakta:
- step_state: new
Step 17: Merge Bakta Output:
- step_state: new
Step 18: ToolDistillator bakta:
- step_state: new
Step 19: ToolDistillator summarize bakta:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - c5da105ec2db5980
- history_state
  - new
- invocation_id
  - c5da105ec2db5980
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': '189f67c4bda79283', 'reason': 'dataset_failed', 'workflow_step_id': 11}]
- workflow_id
  - c5da105ec2db5980

github-actions · 2026-02-07T22:37:52Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ bacterial_genome_annotation.ga_0

Problems:

No path specified for expected output file [integronfinder2_logfile_text]

No path specified for expected output file [integronfinder2_summary]

No path specified for expected output file [integronfinder2_results_tabular]

No path specified for expected output file [bakta_hypothetical_tabular]

No path specified for expected output file [bakta_annotation_json]

No path specified for expected output file [bakta_annotation_tabular]

No path specified for expected output file [isescan_results_tabular]

No path specified for expected output file [isescan_summary_tabular]

No path specified for expected output file [isescan_logfile_text]

No path specified for expected output file [plasmidfinder_result_json]

No path specified for expected output file [plasmidfinder_results_tabular]

No path specified for expected output file [tooldistillator_summarize_annotation_without_bakta]

No path specified for expected output file [tooldistillator_summarize_bakta]

Workflow invocation details

Invocation Messages

Steps

Step 1: Plasmid detection database:
- step_state: scheduled
Step 2: Bacterial genome annotation database:
- step_state: scheduled
Step 3: AMRFinderPlus database:
- step_state: scheduled
Step 4: Run ToolDistillator without bakta:
- step_state: scheduled
Step 5: Run ToolDistillator with only bakta:
- step_state: scheduled
Step 6: Run Bakta:
- step_state: scheduled
Step 7: Sequence collection:
- step_state: scheduled

Step 8: PlasmidFinder for plasmid detection (toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/plasmidfinder:2.1.6--py314hdfd78af_2

Command Line:

mkdir output_dir && mkdir temp_dir && plasmidfinder.py -i '/tmp/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.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 Error:

/usr/local/bin/plasmidfinder.py:351: DeprecationWarning: Use shutil.which instead of find_executable
  if find_executable(method_path) is None:

Standard Output:

{'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 '
                                                                                                                                                                                                                                                                  'date=20240530',
                                                                                                                                                                                                                                                   'coverage': 100.0,
                                                                                                                                                                                                                                                   'hit_id': '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',
                                                                                                                                                                                                                                                   'identity': 100.0,
                                                                                                                                                                                                                                                   'note': 'repB(pE394)',
                                                                                                                                                                                                                                                   'plasmid': 'repUS40',
                                                                                                                                                                                                                                                   'position_in_ref': '1..1158',
                                                                                                                                                                                                                                                   'positions_in_contig': '21156..22313',
                                                                                                                                                                                                                                                   'template_length': 1158}},
                                                 'RepA_N': {'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': {'HSP_length': 1014,
                                                                                                                                                                                                                                                  'accession': 'CP002494',
                                                                                                                                                                                                                                                  'contig_name': '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',
                                                                                                                                                                                                                                                  'coverage': 100.0,
                                                                                                                                                                                                                                                  'hit_id': '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',
                                                                                                                                                                                                                                                  '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': '07.02.2026', 'time': '21:53:06'},
                   'user_input': {'file_format': 'fasta',
                                  'filename(s)': ['/tmp/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.dat'],
                                  'method': 'blast'}}}

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input	`{"database_name": "plasmidfinder_81c11f4_2023_12_04", "input_file": {"values": [{"id": 1, "src": "dce"}]}}`
options	`{"min_cov": "0.6", "threshold": "0.95"}`
output_files	`{"output_selection": ["hit_fasta", "plasmid_fasta", "result_tsv", "result_txt", "data_json"]}`

Step 9: ISEScan for insertion sequence elements detection (toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/isescan:1.7.3--h7b50bb2_0

Command Line:

ln -s '/tmp/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.dat' input && isescan.py --seqfile input --output 'results'  --nthread ${GALAXY_SLOTS:-7}  | tee '/tmp/tmpoaf1g7_4/job_working_directory/000/3/outputs/dataset_4c9d522d-845c-4d12-8a95-47b6da7c5226.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) = 3.3 sec
Time elapsed: 0 hours 0 minutes and 4 seconds.
ISEScan starts at Sat Feb  7 21:53:10 2026
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. Sat Feb  7 21:53:14 2026

Begin to phmmer search against proteome database. Sat Feb  7 21:53:14 2026
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. Sat Feb  7 22:04:27 2026

Begin to profile HMM search against proteome database. Sat Feb  7 22:04:27 2026
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. Sat Feb  7 22:14:39 2026
pred begins at Sat Feb  7 22:14:39 2026
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 Sat Feb  7 22:14:44 2026
Finish addNonORFcopy at Sat Feb  7 22:14:44 2026
Begin addNonORFcopy1 at Sat Feb  7 22:14:48 2026
Finish addNonORFcopy1 at Sat Feb  7 22:14:48 2026
getFullIS() begins at Sat Feb  7 22:14:48 2026
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 Sat Feb  7 22:14:48 2026
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 Sat Feb  7 22:14:48 2026
Begin reading protein database at Sat Feb  7 22:14:48 2026
Finish reading protein database at Sat Feb  7 22:14:48 2026
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 Sat Feb  7 22:14:48 2026
Both complete and partial IS elements are reported.
ISEScan ends at Sat Feb  7 22:14:48 2026

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
log_activate	`true`
remove_short_is	`false`

Step 10: Integron Finder for integrons detection (toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/integron_finder:2.0.5--pyhdfd78af_0

Command Line:

integron_finder '/tmp/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.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/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.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/tmpoaf1g7_4/job_working_directory/000/4/working/Results_Integron_Finder_dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad/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/tmpoaf1g7_4/job_working_directory/000/4/working/Results_Integron_Finder_dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad/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/tmpoaf1g7_4/job_working_directory/000/4/working/Results_Integron_Finder_dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad/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/tmpoaf1g7_4/job_working_directory/000/4/working/Results_Integron_Finder_dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad/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/tmpoaf1g7_4/job_working_directory/000/4/working/Results_Integron_Finder_dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad/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/tmpoaf1g7_4/job_working_directory/000/4/working/Results_Integron_Finder_dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad/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__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/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 11: Bakta functionnal annotation (toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/bakta:1.9.4--pyhdfd78af_0

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/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.dat' | tee 'XXXX'

Exit Code:

```
0
```

Standard Output:

Bakta v1.9.4
Options and arguments:
	input: /tmp/tmpoaf1g7_4/files/f/8/9/dataset_f891daa2-2c13-46c8-b5a8-0580fa27c8ad.dat
	db: /tmp/tmpoaf1g7_4/job_working_directory/000/5/working/database_path, version 5.0, full
	output: /tmp/tmpoaf1g7_4/job_working_directory/000/5/working/bakta_output
	tmp directory: /tmp/tmpoaf1g7_4/job_working_directory/000/5/tmp/tmptufeaw39
	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/tmpoaf1g7_4/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 42:41 [mm:ss].

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmpoaf1g7_4/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": "dce"}]}, "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 12: ToolDistillator without bakta (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/tooldistillator:1.0.4--pyh7e72e81_0

Command Line:

set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator plasmidfinder --hid '8' '/tmp/tmpoaf1g7_4/files/f/7/4/dataset_f741d707-3026-4dc4-8fa3-085b03bf4574.dat' --analysis_software_version '2.1.6+galaxy1' --reference_database_version 'plasmidfinder_81c11f4_2023_12_04' --plasmid_result_tabular_path '/tmp/tmpoaf1g7_4/files/c/6/6/dataset_c66c056e-a918-4c2b-b243-cd4e39e10f53.dat' --plasmid_result_tabular_hid '11' --genome_hit_path '/tmp/tmpoaf1g7_4/files/1/2/4/dataset_124e6fc9-6e98-4713-a606-032cb725521c.dat' --genome_hit_hid '9' --plasmid_hit_path '/tmp/tmpoaf1g7_4/files/6/2/e/dataset_62e5267b-e577-4aea-828e-478636e7e138.dat' --plasmid_hit_hid '10' -o 'tooldistillator_folder/plasmidfinder_0_output.json' | tee 'XXXX' &&  tooldistillator isescan --hid '22' '/tmp/tmpoaf1g7_4/files/2/e/8/dataset_2e871172-dc99-45aa-b2b0-4fd0c4a61616.dat' --analysis_software_version '1.7.3+galaxy0' --reference_database_version '' -o 'tooldistillator_folder/isescan_1_output.json' | tee 'XXXX' &&  tooldistillator integronfinder2 --hid '31' '/tmp/tmpoaf1g7_4/files/a/d/b/dataset_adb6bfc1-160f-4cea-b7de-0094a97013aa.dat' --analysis_software_version '2.0.5+galaxy0' --reference_database_version '' -o 'tooldistillator_folder/integronfinder2_2_output.json' | tee 'XXXX'

Exit Code:

```
0
```

Standard Error:

+ mkdir tooldistillator_folder
+ tooldistillator plasmidfinder --hid 8 /tmp/tmpoaf1g7_4/files/f/7/4/dataset_f741d707-3026-4dc4-8fa3-085b03bf4574.dat --analysis_software_version 2.1.6+galaxy1 --reference_database_version plasmidfinder_81c11f4_2023_12_04 --plasmid_result_tabular_path /tmp/tmpoaf1g7_4/files/c/6/6/dataset_c66c056e-a918-4c2b-b243-cd4e39e10f53.dat --plasmid_result_tabular_hid 11 --genome_hit_path /tmp/tmpoaf1g7_4/files/1/2/4/dataset_124e6fc9-6e98-4713-a606-032cb725521c.dat --genome_hit_hid 9 --plasmid_hit_path /tmp/tmpoaf1g7_4/files/6/2/e/dataset_62e5267b-e577-4aea-828e-478636e7e138.dat --plasmid_hit_hid 10 -o tooldistillator_folder/plasmidfinder_0_output.json
+ tee XXXX
02/07/2026 10:15:21 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/f/7/4/dataset_f741d707-3026-4dc4-8fa3-085b03bf4574.dat
02/07/2026 10:15:21 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/1/2/4/dataset_124e6fc9-6e98-4713-a606-032cb725521c.dat
02/07/2026 10:15:21 PM: plasmidfinderio.py: Analysis of genome_hit_path
02/07/2026 10:15:21 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/6/2/e/dataset_62e5267b-e577-4aea-828e-478636e7e138.dat
02/07/2026 10:15:21 PM: plasmidfinderio.py: Analysis of plasmid_hit_path
+ tooldistillator isescan --hid 22 /tmp/tmpoaf1g7_4/files/2/e/8/dataset_2e871172-dc99-45aa-b2b0-4fd0c4a61616.dat --analysis_software_version 1.7.3+galaxy0 --reference_database_version '' -o tooldistillator_folder/isescan_1_output.json
+ tee XXXX
02/07/2026 10:15:23 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/2/e/8/dataset_2e871172-dc99-45aa-b2b0-4fd0c4a61616.dat
02/07/2026 10:15:23 PM: interfaces.py: No information for orf_fna_path: Not analyzed
02/07/2026 10:15:23 PM: interfaces.py: No information for orf_faa_path: Not analyzed
02/07/2026 10:15:23 PM: interfaces.py: No information for is_fna_path: Not analyzed
02/07/2026 10:15:23 PM: interfaces.py: No information for summary_path: Not analyzed
02/07/2026 10:15:23 PM: interfaces.py: No information for annotation_path: Not analyzed
+ tooldistillator integronfinder2 --hid 31 /tmp/tmpoaf1g7_4/files/a/d/b/dataset_adb6bfc1-160f-4cea-b7de-0094a97013aa.dat --analysis_software_version 2.0.5+galaxy0 --reference_database_version '' -o tooldistillator_folder/integronfinder2_2_output.json
+ tee XXXX
02/07/2026 10:15:25 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/a/d/b/dataset_adb6bfc1-160f-4cea-b7de-0094a97013aa.dat
/usr/local/lib/python3.14/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)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/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": 3, "src": "dce"}]}, "input": {"values": [{"id": 2, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "plasmid_hit_path": {"values": [{"id": 4, "src": "dce"}]}, "plasmid_result_tabular_path": {"values": [{"id": 5, "src": "dce"}]}, "reference_database_version": "plasmidfinder_81c11f4_2023_12_04", "tool_list": "plasmidfinder"}}, {"__index__": 1, "select_tool": {"__current_case__": 22, "annotation_path": null, "input": {"values": [{"id": 9, "src": "dce"}]}, "is_fna_path": null, "orf_faa_path": null, "orf_fna_path": null, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "summary_path": null, "tool_list": "isescan"}}, {"__index__": 2, "select_tool": {"__current_case__": 21, "input": {"values": [{"id": 15, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "summary_file_path": null, "tool_list": "integronfinder2"}}]}

Step 13: Format Bakta output (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.3.1
```

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpoaf1g7_4/job_working_directory/000/9/configs/tmpz4ped515' '/tmp/tmpoaf1g7_4/files/4/b/d/dataset_4bd2927a-2561-42db-b791-411d34523d68.dat' > '/tmp/tmpoaf1g7_4/job_working_directory/000/9/outputs/dataset_3d067976-c14a-4a6b-aef3-4f4b7dd4392b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN {\n print \"Annotation\\tCount\"\n}\n\n/^Annotation:/ { in_block = 1; next }\n/^Bakta:/ { in_block = 0 }\n\nin_block {\n if ($0 ~ /^[[:space:]]$/) next # skip blank lines\n sub(/[[:space:]]:[[:space:]]*/, \"\\t\", $0) # replace first colon+spaces with a tab\n print $0\n}"`
dbkey	`"?"`
variables	`[]`

Step 14: Pick the main bakta file if the tool is run. (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 27, "src": "dce"}]}}]}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/multiqc:1.33--pyhdfd78af_0

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/bakta_0 &&     ln -s '/tmp/tmpoaf1g7_4/files/4/b/d/dataset_4bd2927a-2561-42db-b791-411d34523d68.dat' 'multiqc_WDir/bakta_0/test_input.txt' &&    multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.33

       file_search | Search path: /tmp/tmpoaf1g7_4/job_working_directory/000/6/working/multiqc_WDir

             bakta | Found 1 logs

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete
cp: cannot stat './report_data/*plot*.txt': No such file or directory

Standard Output:

total 612
-rw-r--r-- 1 1001 1001    156 Feb  7 22:36 bakta_feature_types.txt
-rw-r--r-- 1 1001 1001   3217 Feb  7 22:36 llms-full.txt
-rw-r--r-- 1 1001 1001   8394 Feb  7 22:36 multiqc.log
-rw-r--r-- 1 1001 1001 533442 Feb  7 22:36 multiqc.parquet
-rw-r--r-- 1 1001 1001    221 Feb  7 22:36 multiqc_bakta.txt
-rw-r--r-- 1 1001 1001    121 Feb  7 22:36 multiqc_citations.txt
-rw-r--r-- 1 1001 1001  49134 Feb  7 22:36 multiqc_data.json
-rw-r--r-- 1 1001 1001     71 Feb  7 22:36 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     25 Feb  7 22:36 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    153 Feb  7 22:36 multiqc_sources.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 35, "input": {"values": [{"id": 26, "src": "hdca"}]}, "software": "bakta"}}]`
title	`""`

Step 16: ToolDistillator summarize without bakta (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/tooldistillator:1.0.4--pyh7e72e81_0

Command Line:

tooldistillator --version && mkdir -p input_files && cp '/tmp/tmpoaf1g7_4/files/6/9/e/dataset_69ef5398-efaf-46ef-9da7-d012025d2f96.dat' ./input_files/ && cp '/tmp/tmpoaf1g7_4/files/d/8/5/dataset_d8506633-8544-40e9-ae47-df8517696a02.dat' ./input_files/ && cp '/tmp/tmpoaf1g7_4/files/5/9/e/dataset_59e307be-12ed-498e-b2b5-6ec03b391d72.dat' ./input_files/ && tooldistillator summarize input_files/* -o summary.json

Exit Code:

```
0
```

Standard Output:

```
tooldistillator 1.0.4
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 17: Merge Bakta Output (toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:8.25--1
```

Command Line:

sh '/tmp/tmpoaf1g7_4/job_working_directory/000/11/configs/tmphsq6b03l'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fill_char	`"."`
has_header	`"1"`
identifier_column	`"1"`
include_outputs	`None`
old_col_in_header	`true`

Step 18: ToolDistillator bakta (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/tooldistillator:1.0.4--pyh7e72e81_0

Command Line:

set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator bakta --hid '68' '/tmp/tmpoaf1g7_4/files/6/a/1/dataset_6a163ac7-83bb-4bf2-b767-36e63cca0d78.dat' --analysis_software_version '1.9.4' --reference_database_version 'V5.0_2023-02-20' --annotation_tabular_path '/tmp/tmpoaf1g7_4/files/6/f/2/dataset_6f2170db-52ae-47a6-a0ed-94777afb30ce.dat' --annotation_tabular_hid '45' --annotation_genbank_path '/tmp/tmpoaf1g7_4/files/5/b/e/dataset_5be1e960-3321-4f27-8a20-88cb044f99d0.dat' --annotation_genbank_hid '47' --summary_result_path '/tmp/tmpoaf1g7_4/files/4/b/d/dataset_4bd2927a-2561-42db-b791-411d34523d68.dat' --summary_result_hid '54' -o 'tooldistillator_folder/bakta_0_output.json' | tee 'XXXX'

Exit Code:

```
0
```

Standard Error:

+ mkdir tooldistillator_folder
+ tooldistillator bakta --hid 68 /tmp/tmpoaf1g7_4/files/6/a/1/dataset_6a163ac7-83bb-4bf2-b767-36e63cca0d78.dat --analysis_software_version 1.9.4 --reference_database_version V5.0_2023-02-20 --annotation_tabular_path /tmp/tmpoaf1g7_4/files/6/f/2/dataset_6f2170db-52ae-47a6-a0ed-94777afb30ce.dat --annotation_tabular_hid 45 --annotation_genbank_path /tmp/tmpoaf1g7_4/files/5/b/e/dataset_5be1e960-3321-4f27-8a20-88cb044f99d0.dat --annotation_genbank_hid 47 --summary_result_path /tmp/tmpoaf1g7_4/files/4/b/d/dataset_4bd2927a-2561-42db-b791-411d34523d68.dat --summary_result_hid 54 -o tooldistillator_folder/bakta_0_output.json
+ tee XXXX
02/07/2026 10:36:13 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/6/a/1/dataset_6a163ac7-83bb-4bf2-b767-36e63cca0d78.dat
02/07/2026 10:36:13 PM: baktaio.py: bakta input file imported
02/07/2026 10:36:13 PM: baktaio.py: summary_result_path analysis
02/07/2026 10:36:13 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/4/b/d/dataset_4bd2927a-2561-42db-b791-411d34523d68.dat
02/07/2026 10:36:13 PM: interfaces.py: Extraction of: annotation_tabular_path
02/07/2026 10:36:13 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/6/f/2/dataset_6f2170db-52ae-47a6-a0ed-94777afb30ce.dat
02/07/2026 10:36:13 PM: interfaces.py: No information for gff_file_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: Extraction of: annotation_genbank_path
02/07/2026 10:36:13 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/5/b/e/dataset_5be1e960-3321-4f27-8a20-88cb044f99d0.dat
02/07/2026 10:36:13 PM: interfaces.py: No information for annotation_embl_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: No information for contig_sequences_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: No information for nucleotide_annotation_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: No information for amino_acid_annotation_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: No information for hypothetical_protein_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: No information for hypothetical_tabular_path: Not analyzed
02/07/2026 10:36:13 PM: interfaces.py: Extraction of: summary_result_path
02/07/2026 10:36:13 PM: interfaces.py: Treatment of /tmp/tmpoaf1g7_4/files/4/b/d/dataset_4bd2927a-2561-42db-b791-411d34523d68.dat
02/07/2026 10:36:13 PM: interfaces.py: No information for plot_file_path: Not analyzed

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
log	`false`
tool_section	{"tools": [{"__index__": 0, "select_tool": {"__current_case__": 3, "amino_acid_annotation_path": null, "annotation_embl_path": null, "annotation_genbank_path": {"values": [{"id": 19, "src": "dce"}]}, "annotation_tabular_path": {"values": [{"id": 17, "src": "dce"}]}, "contig_sequences_path": null, "gff_file_path": null, "hypothetical_protein_path": null, "hypothetical_tabular_path": null, "input": {"values": [{"id": 35, "src": "dce"}]}, "nucleotide_annotation_path": null, "origin": {"__current_case__": 0, "analysis_software_version": "1.9.4", "origin": "true"}, "plot_file_path": null, "reference_database_version": "V5.0_2023-02-20", "summary_result_path": {"values": [{"id": 26, "src": "dce"}]}, "tool_list": "bakta"}}]}

Step 19: ToolDistillator summarize bakta (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/tooldistillator:1.0.4--pyh7e72e81_0

Command Line:

tooldistillator --version && mkdir -p input_files && cp '/tmp/tmpoaf1g7_4/files/2/e/5/dataset_2e5fc5b0-acb3-48f0-87de-d16752a598b5.dat' ./input_files/ && tooldistillator summarize input_files/* -o summary.json

Exit Code:

```
0
```

Standard Output:

```
tooldistillator 1.0.4
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3c22a8ec046f11f189517c1e5241c10b"`
chromInfo	`"/tmp/tmpoaf1g7_4/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Other invocation details
- history_id
  - 52879c3fd8ae89c2
- history_state
  - ok
- invocation_id
  - 52879c3fd8ae89c2
- invocation_state
  - scheduled
- workflow_id
  - 52879c3fd8ae89c2

github-actions · 2026-02-08T19:23:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ bacterial_genome_annotation.ga_0

SantaMcCloud · 2026-02-08T19:29:38Z

hm idk why this is failing i did run this wihtout error

Update bacterial_genome_annotation WF

f642bd6

SantaMcCloud added 2 commits February 7, 2026 21:52

add identifier line

defcc4c

add new file for test

49cba02

fix linting

31519ce

little changes

7f3f43e

Provide feedback

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Update bacterial_genome_annotation WF#1099

Update bacterial_genome_annotation WF#1099
SantaMcCloud wants to merge 5 commits intogalaxyproject:mainfrom
SantaMcCloud:update_bac_annot_wf

SantaMcCloud commented Feb 7, 2026

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SantaMcCloud commented Feb 7, 2026

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