Updating workflows/microbiome/metagenomic-raw-reads-amr-analysis from 1.2 to 1.3 by gxydevbot · Pull Request #1314 · galaxyproject/iwc

gxydevbot · 2026-07-20T09:04:06Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2

The workflow release number has been updated from 1.2 to 1.3.

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

… 1.2 to 1.3

Updated version number and date for the changelog.

hugolefeuvre

Looks good to me

github-actions · 2026-07-20T10:09:00Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ metagenomic-raw-reads-amr-analysis.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Metagenomics Reads after Quality Control and Host/Contamination Removal:
- step_state: scheduled
Step 2: Taxonomy Profiling Database for Sylph:
- step_state: scheduled
Step 3: ARG Database for Groot:
- step_state: scheduled
Step 4: Taxonomic Information Database for Sylph:
- step_state: scheduled
Step 5: Average Read Length for Groot:
- step_state: scheduled
Step 6: Coverage Threshold for Groot to Report an ARG:
- step_state: scheduled
Step 7: ARG Database used by Groot for ARGnorm:
- step_state: scheduled
Step 8: Minimum probability for considering a reads as ARG-like in deepARG:
- step_state: scheduled

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.5
```

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpra7ms2y_/job_working_directory/000/3/outputs/dataset_b4301477-d080-4d33-8b79-a2da17d89a80.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpra7ms2y_/job_working_directory/000/3/outputs/dataset_b4301477-d080-4d33-8b79-a2da17d89a80.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 10: ARG Database for DeepARG:
- step_state: scheduled
Step 11: Unlabelled step (__UNZIP_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "bb574152841e11f18ae06045bd4a52bb"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpra7ms2y_/job_working_directory/000/5/configs/tmp_stg4msf' '/tmp/tmpra7ms2y_/job_working_directory/000/5/outputs/dataset_e2709553-c8c7-49c3-8ed4-14d9216b8f82.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-faf39a849844225d3e8e207461b41267d626ea2c:28d93c720a3f8d81e77088e242ed05a32d5aaeff-0

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/OceanDNA-c200-v0.3.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmpra7ms2y_/files/0/5/b/dataset_05b9a950-6f1c-4582-951c-d3c455aee357.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmpra7ms2y_/files/f/8/a/dataset_f8acac2f-4a2a-40ba-b635-6b876e965164.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpra7ms2y_/job_working_directory/000/6/outputs/dataset_ac06e69d-69e3-41a2-bcf2-6027702a7f48.dat'  && cp '/tmp/tmpra7ms2y_/job_working_directory/000/6/configs/tmpthj6xpmm' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmpra7ms2y_/job_working_directory/000/6/outputs/dataset_ac06e69d-69e3-41a2-bcf2-6027702a7f48.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata OceanDNA && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
0
```

Standard Error:

2026-07-20T09:39:02.844Z INFO  [sylph::sketch] Sketching paired sequences...
2026-07-20T09:39:03.026Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2026-07-20T09:39:03.026Z INFO  [sylph::sketch] Finished.
2026-07-20T09:39:03.029Z INFO  [sylph::contain] Obtaining sketches...
2026-07-20T09:39:12.076Z INFO  [sylph::contain] Finished obtaining genome sketches.
2026-07-20T09:39:12.775Z INFO  [sylph::contain] sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp taxonomic profiling; reassigning k-mers for 1 genomes...
2026-07-20T09:39:12.782Z INFO  [sylph::contain] sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp has 1 genomes passing profiling threshold. 
2026-07-20T09:39:12.782Z INFO  [sylph::contain] Finished sample sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp.
2026-07-20T09:39:12.782Z INFO  [sylph::contain] sylph finished.

Standard Output:

Reading metadata: ['OceanDNA'] ...
Processing sylph output file:  /tmp/tmpra7ms2y_/job_working_directory/000/6/outputs/dataset_ac06e69d-69e3-41a2-bcf2-6027702a7f48.dat
Writing output to: sylph_taxprof_out/sylph_tax_out-raw_reads_metag_test.fastq.gz.sylphmpa ...
Merged data written to output_tax_merge.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_12122025_OceanDNA-c200-v0.3.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-3a61021420fe1ff4decc0ee3c93af981013e4f83:bd2b2721586ed321422add5fa76b9154d9039358-0

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmpra7ms2y_/files/0/5/b/dataset_05b9a950-6f1c-4582-951c-d3c455aee357.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmpra7ms2y_/files/f/8/a/dataset_f8acac2f-4a2a-40ba-b635-6b876e965164.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 127500 Both Surviving: 127500 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    127500  Pairs
     69309  Merged (54.4%)
     58191  Not merged (45.6%)

Pairs that failed merging due to various reasons:
     41302  too few kmers found on same diagonal
       265  multiple potential alignments
     12318  alignment score too low, or score drop too high
       295  overlap too short
      4011  staggered read pairs

Statistics of all reads:
     92.00  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 857
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.003s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1318reads [00:00, 274933.74reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:06,  6.16s/chunks]
1chunks [00:06,  6.16s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/145 [00:00<?, ?it/s]
100%|██████████| 145/145 [00:00<00:00, 41428.75it/s]
185691 reads; of these:
  185691 (100.00%) were unpaired; of these:
    185385 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    306 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 15: Concatenate files R1 and R2 (cat1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

cat '/tmp/tmpra7ms2y_/files/0/5/b/dataset_05b9a950-6f1c-4582-951c-d3c455aee357.dat' '/tmp/tmpra7ms2y_/files/f/8/a/dataset_f8acac2f-4a2a-40ba-b635-6b876e965164.dat' > '/tmp/tmpra7ms2y_/job_working_directory/000/8/outputs/dataset_bedfc413-1003-48f7-b9b8-a66fef0986f5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "input2": {"values": [{"id": 5, "src": "dce"}]}}]`

Step 16: Unlabelled step (__FLATTEN__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "bb574152841e11f18ae06045bd4a52bb"
      
      input {"values": [{"id": 4, "src": "hdca"}]}
      
      join_identifier "_"

Step 17: argNorm on DeepARG ouput (toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/argnorm:1.0.0--pyhdfd78af_0

Command Line:

argnorm 'deeparg' -i '/tmp/tmpra7ms2y_/files/e/8/6/dataset_e867a323-d09f-474c-8848-589059dd702a.dat' -o '/tmp/tmpra7ms2y_/job_working_directory/000/9/outputs/dataset_9034c5cf-b6ce-431f-b014-712fbee27524.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpra7ms2y_/job_working_directory/000/9/outputs/dataset_9034c5cf-b6ce-431f-b014-712fbee27524.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 18: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/groot:1.1.2--h047eeb3_7

Command Line:

set -x pipefail; ln -s -f '/tmp/tmpra7ms2y_/files/b/e/d/dataset_bedfc413-1003-48f7-b9b8-a66fef0986f5.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmpra7ms2y_/job_working_directory/000/10/outputs/dataset_1bab43c8-7635-4edb-9e63-828871481050.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmpra7ms2y_/files/b/e/d/dataset_bedfc413-1003-48f7-b9b8-a66fef0986f5.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1
+ groot report --covCutoff 0.6

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 19: Unlabelled step (Remove beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

tail -n '+2' '/tmp/tmpra7ms2y_/files/f/4/3/dataset_f43b21bc-4aba-4789-b9b6-db98578d3ec9.dat' > '/tmp/tmpra7ms2y_/job_working_directory/000/15/outputs/dataset_f5f7beb8-0a27-4a13-9947-ee6832d8832b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
num_lines	`"1"`

Step 20: Unlabelled step (__RELABEL_FROM_FILE__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 6, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 19, "src": "hdca"}]}`

Step 21: Unlabelled step (Remove beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

tail -n '+2' '/tmp/tmpra7ms2y_/files/9/0/3/dataset_9034c5cf-b6ce-431f-b014-712fbee27524.dat' > '/tmp/tmpra7ms2y_/job_working_directory/000/11/outputs/dataset_6012572b-d1a9-463c-87ab-f601f08d3516.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
num_lines	`"1"`

Step 22: argNorm on Groot output (toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/argnorm:1.0.0--pyhdfd78af_0

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmpra7ms2y_/files/1/b/a/dataset_1bab43c8-7635-4edb-9e63-828871481050.dat' -o '/tmp/tmpra7ms2y_/job_working_directory/000/12/outputs/dataset_522e1f29-8cb0-4df6-9e7e-4d73a29bc6b3.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpra7ms2y_/job_working_directory/000/12/outputs/dataset_522e1f29-8cb0-4df6-9e7e-4d73a29bc6b3.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 23: Unlabelled step (toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/3.0.2+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-3ddac2a0bed96a62f10083cc86942c16ca30a274:88f4febb36ab6bca7fffa8db3d0fe6226929ad60-0

Command Line:

python3 '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/761f8ab8fdb6/table_pandas_rename_column/table_pandas_rename_column.py' --input_dataset '/tmp/tmpra7ms2y_/files/6/0/1/dataset_6012572b-d1a9-463c-87ab-f601f08d3516.dat' 'tabular' --rename 1=ARG --output_dataset '/tmp/tmpra7ms2y_/job_working_directory/000/13/outputs/dataset_e32abbc2-ab9b-4ef4-8eae-d15c532085fb.dat' 'tabular'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columns_selection	`[{"__index__": 0, "column": "1", "new_name": "ARG"}]`
dbkey	`"?"`

Step 24: Unlabelled step (__FILTER_FAILED_DATASETS__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "bb574152841e11f18ae06045bd4a52bb"
      
      input {"values": [{"id": 17, "src": "hdca"}]}

Step 25: Unlabelled step (Remove beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/coreutils:8.31--h14c3975_0

Command Line:

tail -n '+2' '/tmp/tmpra7ms2y_/files/5/2/2/dataset_522e1f29-8cb0-4df6-9e7e-4d73a29bc6b3.dat' > '/tmp/tmpra7ms2y_/job_working_directory/000/18/outputs/dataset_c9726bcd-c79b-4136-a619-aed2da19af77.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
num_lines	`"1"`

Step 26: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.6+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/tooldistillator:1.0.6--pyh106432d_0

Command Line:

set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator groot --hid '32' '/tmp/tmpra7ms2y_/files/1/b/a/dataset_1bab43c8-7635-4edb-9e63-828871481050.dat' --analysis_software_version '1.1.2+galaxy2' --reference_database_version 'arg-annot.90-1.1.2-08112025' -o 'tooldistillator_folder/groot_0_output.json' | tee 'XXXX' &&  tooldistillator sylph --hid '13' '/tmp/tmpra7ms2y_/files/a/c/0/dataset_ac06e69d-69e3-41a2-bcf2-6027702a7f48.dat' --analysis_software_version '0.8.1+galaxy0' --reference_database_version 'sylph_downloaded_12122025_OceanDNA-c200-v0.3.syldb' -o 'tooldistillator_folder/sylph_1_output.json' | tee 'XXXX' &&  tooldistillator sylphtax --hid '14' '/tmp/tmpra7ms2y_/files/5/3/d/dataset_53d7a123-599a-4b02-9e78-5cec1ccf604e.dat' --analysis_software_version '0.8.1+galaxy0' --reference_database_version 'sylph_tax_downloaded_08112025' -o 'tooldistillator_folder/sylphtax_2_output.json' | tee 'XXXX' &&  tooldistillator argnorm --hid '46' '/tmp/tmpra7ms2y_/files/5/2/2/dataset_522e1f29-8cb0-4df6-9e7e-4d73a29bc6b3.dat' --analysis_software_version '' --reference_database_version '' -o 'tooldistillator_folder/argnorm_3_output.json' | tee 'XXXX' &&  tooldistillator tabular_file --hid '43' '/tmp/tmpra7ms2y_/files/f/5/f/dataset_f5f7beb8-0a27-4a13-9947-ee6832d8832b.dat' --analysis_software_version '1.0.0' --reference_database_version 'sylph_tax_downloaded_08112025' --analysis_software_name 'sylph-tax.sylphmpa_file' -o 'tooldistillator_folder/tabular_file_4_output.json' | tee 'XXXX' &&  tooldistillator deeparg --hid '21' '/tmp/tmpra7ms2y_/files/e/8/6/dataset_e867a323-d09f-474c-8848-589059dd702a.dat' --analysis_software_version '1.0.4+galaxy1' --reference_database_version 'deeparg_1.0.4-07112025' --report_ARG_merged_path '/tmp/tmpra7ms2y_/files/2/6/0/dataset_26011fad-ca1f-4b30-8d76-1b7b26f990a1.dat' --report_ARG_merged_hid '22' --report_ARG_merged_quant_subtype_path '/tmp/tmpra7ms2y_/files/6/b/8/dataset_6b814054-f5da-425b-9fa5-857864e8162f.dat' --report_ARG_merged_quant_subtype_hid '23' --report_ARG_merged_quant_type_path '/tmp/tmpra7ms2y_/files/3/5/7/dataset_357cc9c9-68e0-4629-96ae-81669a0dcde3.dat' --report_ARG_merged_quant_type_hid '24' -o 'tooldistillator_folder/deeparg_5_output.json' | tee 'XXXX' &&  tooldistillator argnorm --hid '30' '/tmp/tmpra7ms2y_/files/9/0/3/dataset_9034c5cf-b6ce-431f-b014-712fbee27524.dat' --analysis_software_version '1.0.0+galaxy0' --reference_database_version '' -o 'tooldistillator_folder/argnorm_6_output.json' | tee 'XXXX'

Exit Code:

```
0
```

Standard Error:

+ mkdir tooldistillator_folder
+ tooldistillator groot --hid 32 /tmp/tmpra7ms2y_/files/1/b/a/dataset_1bab43c8-7635-4edb-9e63-828871481050.dat --analysis_software_version 1.1.2+galaxy2 --reference_database_version arg-annot.90-1.1.2-08112025 -o tooldistillator_folder/groot_0_output.json
+ tee XXXX
07/20/2026 09:44:09 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/1/b/a/dataset_1bab43c8-7635-4edb-9e63-828871481050.dat
07/20/2026 09:44:09 AM: grootio.py: add Groot report file
+ tooldistillator sylph --hid 13 /tmp/tmpra7ms2y_/files/a/c/0/dataset_ac06e69d-69e3-41a2-bcf2-6027702a7f48.dat --analysis_software_version 0.8.1+galaxy0 --reference_database_version sylph_downloaded_12122025_OceanDNA-c200-v0.3.syldb -o tooldistillator_folder/sylph_1_output.json
+ tee XXXX
07/20/2026 09:44:10 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/a/c/0/dataset_ac06e69d-69e3-41a2-bcf2-6027702a7f48.dat
07/20/2026 09:44:10 AM: sylphio.py: add Sylph report file
+ tooldistillator sylphtax --hid 14 /tmp/tmpra7ms2y_/files/5/3/d/dataset_53d7a123-599a-4b02-9e78-5cec1ccf604e.dat --analysis_software_version 0.8.1+galaxy0 --reference_database_version sylph_tax_downloaded_08112025 -o tooldistillator_folder/sylphtax_2_output.json
+ tee XXXX
07/20/2026 09:44:11 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/5/3/d/dataset_53d7a123-599a-4b02-9e78-5cec1ccf604e.dat
07/20/2026 09:44:11 AM: sylphtaxio.py: add Sylph-tax merge report file
+ tooldistillator argnorm --hid 46 /tmp/tmpra7ms2y_/files/5/2/2/dataset_522e1f29-8cb0-4df6-9e7e-4d73a29bc6b3.dat --analysis_software_version '' --reference_database_version '' -o tooldistillator_folder/argnorm_3_output.json
+ tee XXXX
07/20/2026 09:44:12 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/5/2/2/dataset_522e1f29-8cb0-4df6-9e7e-4d73a29bc6b3.dat
07/20/2026 09:44:12 AM: argnormio.py: add argNorm report file
+ tooldistillator tabular_file --hid 43 /tmp/tmpra7ms2y_/files/f/5/f/dataset_f5f7beb8-0a27-4a13-9947-ee6832d8832b.dat --analysis_software_version 1.0.0 --reference_database_version sylph_tax_downloaded_08112025 --analysis_software_name sylph-tax.sylphmpa_file -o tooldistillator_folder/tabular_file_4_output.json
+ tee XXXX
07/20/2026 09:44:13 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/f/5/f/dataset_f5f7beb8-0a27-4a13-9947-ee6832d8832b.dat
+ tooldistillator deeparg --hid 21 /tmp/tmpra7ms2y_/files/e/8/6/dataset_e867a323-d09f-474c-8848-589059dd702a.dat --analysis_software_version 1.0.4+galaxy1 --reference_database_version deeparg_1.0.4-07112025 --report_ARG_merged_path /tmp/tmpra7ms2y_/files/2/6/0/dataset_26011fad-ca1f-4b30-8d76-1b7b26f990a1.dat --report_ARG_merged_hid 22 --report_ARG_merged_quant_subtype_path /tmp/tmpra7ms2y_/files/6/b/8/dataset_6b814054-f5da-425b-9fa5-857864e8162f.dat --report_ARG_merged_quant_subtype_hid 23 --report_ARG_merged_quant_type_path /tmp/tmpra7ms2y_/files/3/5/7/dataset_357cc9c9-68e0-4629-96ae-81669a0dcde3.dat --report_ARG_merged_quant_type_hid 24 -o tooldistillator_folder/deeparg_5_output.json
+ tee XXXX
07/20/2026 09:44:14 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/e/8/6/dataset_e867a323-d09f-474c-8848-589059dd702a.dat
07/20/2026 09:44:14 AM: deepargio.py: add DeepARG report file
07/20/2026 09:44:14 AM: deepargio.py: add DeepARG ARG merged report file
07/20/2026 09:44:14 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/2/6/0/dataset_26011fad-ca1f-4b30-8d76-1b7b26f990a1.dat
07/20/2026 09:44:14 AM: deepargio.py: add DeepARG ARG merged quant subtype report file
07/20/2026 09:44:14 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/6/b/8/dataset_6b814054-f5da-425b-9fa5-857864e8162f.dat
07/20/2026 09:44:14 AM: deepargio.py: add DeepARG ARG merged quant type report file
07/20/2026 09:44:14 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/3/5/7/dataset_357cc9c9-68e0-4629-96ae-81669a0dcde3.dat
+ tooldistillator argnorm --hid 30 /tmp/tmpra7ms2y_/files/9/0/3/dataset_9034c5cf-b6ce-431f-b014-712fbee27524.dat --analysis_software_version 1.0.0+galaxy0 --reference_database_version '' -o tooldistillator_folder/argnorm_6_output.json
+ tee XXXX
07/20/2026 09:44:15 AM: interfaces.py: Treatment of /tmp/tmpra7ms2y_/files/9/0/3/dataset_9034c5cf-b6ce-431f-b014-712fbee27524.dat
07/20/2026 09:44:15 AM: argnormio.py: add argNorm report file

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
log	`false`
tool_section	{"tools": [{"__index__": 0, "select_tool": {"__current_case__": 19, "bam_file_path": null, "groot_log_path": null, "input": {"values": [{"id": 17, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "arg-annot.90-1.1.2-08112025", "tool_list": "groot"}}, {"__index__": 1, "select_tool": {"__current_case__": 38, "input": {"values": [{"id": 7, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "sylph_downloaded_12122025_OceanDNA-c200-v0.3.syldb", "tool_list": "sylph"}}, {"__index__": 2, "select_tool": {"__current_case__": 39, "input": {"values": [{"id": 8, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "sylph_tax_downloaded_08112025", "taxonomic_profile_folder_path": null, "tool_list": "sylphtax"}}, {"__index__": 3, "select_tool": {"__current_case__": 2, "input": {"values": [{"id": 25, "src": "dce"}]}, "origin": {"__current_case__": 0, "analysis_software_version": null, "origin": "true"}, "reference_database_version": null, "tool_list": "argnorm"}}, {"__index__": 4, "select_tool": {"__current_case__": 40, "analysis_software_name": "sylph-tax.sylphmpa_file", "input": {"values": [{"id": 23, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "sylph_tax_downloaded_08112025", "tool_list": "tabular_file"}}, {"__index__": 5, "select_tool": {"__current_case__": 12, "bam_clean_file_path": null, "bam_clean_sorted_file_path": null, "daa_clean_align_file_path": null, "input": {"values": [{"id": 9, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "deeparg_1.0.4-07112025", "report_arg_merged_path": {"values": [{"id": 10, "src": "dce"}]}, "report_arg_merged_quant_subtype_path": {"values": [{"id": 11, "src": "dce"}]}, "report_arg_merged_quant_type_path": {"values": [{"id": 12, "src": "dce"}]}, "report_potential_arg_path": null, "sam_clean_file_path": null, "sequence_clean_file_path": null, "tool_list": "deeparg"}}, {"__index__": 6, "select_tool": {"__current_case__": 2, "input": {"values": [{"id": 16, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "tool_list": "argnorm"}}]}

Step 27: Unlabelled step (toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/3.0.2+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-3ddac2a0bed96a62f10083cc86942c16ca30a274:88f4febb36ab6bca7fffa8db3d0fe6226929ad60-0

Command Line:

python3 '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/761f8ab8fdb6/table_pandas_rename_column/table_pandas_rename_column.py' --input_dataset '/tmp/tmpra7ms2y_/files/c/9/7/dataset_c9726bcd-c79b-4136-a619-aed2da19af77.dat' 'tabular' --rename 1=ARG 2=Read_Count 3=Gene_Length 4=Coverage_CIGARlike_representation --output_dataset '/tmp/tmpra7ms2y_/job_working_directory/000/20/outputs/dataset_4ddc66a2-de50-4395-ae31-ee81b11a0d48.dat' 'tabular'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columns_selection	`[{"__index__": 0, "column": "1", "new_name": "ARG"}, {"__index__": 1, "column": "2", "new_name": "Read_Count"}, {"__index__": 2, "column": "3", "new_name": "Gene_Length"}, {"__index__": 3, "column": "4", "new_name": "Coverage_(CIGAR-like_representation)"}]`
dbkey	`"?"`

Step 28: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.6+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/tooldistillator:1.0.6--pyh106432d_0

Command Line:

tooldistillator --version && mkdir -p input_files && cp '/tmp/tmpra7ms2y_/files/2/9/4/dataset_294e0bca-980c-4b4a-b267-d53c9bb18d51.dat' ./input_files/ && cp '/tmp/tmpra7ms2y_/files/7/9/f/dataset_79f5dbfa-b7c2-420a-a99f-97fd505db8d6.dat' ./input_files/ && cp '/tmp/tmpra7ms2y_/files/7/d/7/dataset_7d700cd5-8a09-4b65-884c-e8b02714a979.dat' ./input_files/ && cp '/tmp/tmpra7ms2y_/files/c/a/f/dataset_caf1a53c-70ca-43d3-9e74-7bc40f82e1e7.dat' ./input_files/ && cp '/tmp/tmpra7ms2y_/files/5/1/2/dataset_512221cb-6e16-4b4e-9d19-7879b7db7cfc.dat' ./input_files/ && cp '/tmp/tmpra7ms2y_/files/f/0/d/dataset_f0dd06a4-8703-4b1c-9342-649d4ce26126.dat' ./input_files/ && cp '/tmp/tmpra7ms2y_/files/2/c/2/dataset_2c214aac-1b36-40d5-9d76-b3ee1db2eb91.dat' ./input_files/ && tooldistillator summarize input_files/* -o summary.json

Exit Code:

```
0
```

Standard Output:

```
tooldistillator 1.0.6
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 29: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/multiqc:1.35--pyhdfd78af_1

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/custom_content_0 &&    ln -s '/tmp/tmpra7ms2y_/files/4/d/d/dataset_4ddc66a2-de50-4395-ae31-ee81b11a0d48.dat' 'multiqc_WDir/custom_content_0/file_0_raw_reads_metag_test' && more /tmp/tmpra7ms2y_/files/4/d/d/dataset_4ddc66a2-de50-4395-ae31-ee81b11a0d48.dat && mkdir multiqc_WDir/custom_content_1 &&    ln -s '/tmp/tmpra7ms2y_/files/e/3/2/dataset_e32abbc2-ab9b-4ef4-8eae-d15c532085fb.dat' 'multiqc_WDir/custom_content_1/file_1_raw_reads_metag_test' && more /tmp/tmpra7ms2y_/files/e/3/2/dataset_e32abbc2-ab9b-4ef4-8eae-d15c532085fb.dat && mkdir multiqc_WDir/sylphtax_2 &&         ln -s '/tmp/tmpra7ms2y_/files/f/4/3/dataset_f43b21bc-4aba-4789-b9b6-db98578d3ec9.dat' 'multiqc_WDir/sylphtax_2/raw_reads_metag_test.sylphmpa'  &&        multiqc multiqc_WDir --filename 'report'      --config '/tmp/tmpra7ms2y_/job_working_directory/000/21/configs/tmp0er4keoq'  && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.35

            config | Loading config settings from: /tmp/tmpra7ms2y_/job_working_directory/000/21/configs/tmp0er4keoq
       file_search | Search path: /tmp/tmpra7ms2y_/job_working_directory/000/21/working/multiqc_WDir
    custom_content | section_0: Found 4 samples (PlotType.TABLE)
    custom_content | section_1: Found 31 samples (PlotType.TABLE)
          sylphtax | Found 1 reports
     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

::::::::::::::
/tmp/tmpra7ms2y_/files/4/d/d/dataset_4ddc66a2-de50-4395-ae31-ee81b11a0d48.dat
::::::::::::::
ARG	Read_Count	Gene_Length	Coverage_CIGARlike_representation	ARO	ARO_name	Cut_Off	confers_resistance_to	confers_resistance_to_names	resistance_to_drug_classes	resistance_to_drug_classes_names
argannot~~~(Bla)cfxA4~~~AY769933:1-966	29	966	14D738M25D168M21D	ARO:3003005	CfxA4	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
argannot~~~(Bla)cfxA~~~U38243:150-1115	29	966	14D865M87D	ARO:3003001	CfxA	Perfect	ARO:0000008,ARO:3004001,ARO:3004004,ARO:3004014,ARO:3009106	cefoxitin,cefmetazole,cefotetan,flomoxef,second-generation cephalosporin	ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007	beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic
argannot~~~(Bla)cfxA5~~~AY769934:28-993	29	966	14D738M25D168M21D	ARO:3003096	CfxA5	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
argannot~~~(Bla)cfxA2~~~AF504910:1-966	29	966	110D376M43D416M21D	ARO:3003002	CfxA2	Strict	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
::::::::::::::
/tmp/tmpra7ms2y_/files/e/3/2/dataset_e32abbc2-ab9b-4ef4-8eae-d15c532085fb.dat
::::::::::::::
ARG	query-start	query-end	read_id	predicted_ARG-class	best-hit	probability	identity	alignment-length	alignment-bitscore	alignment-evalue	counts	ARO	ARO_name	Cut_Off	confers_resistance_to	confers_resistance_to_names	resistance_to_drug_classes	resistance_to_drug_classes_names
CFXA2	38	70	CAU6DANXX170407:3:1115:8843:53419/1	beta-lactam	U38243.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	0.9999999999999952	100.0	33	67.4	2.83e-16	1	ARO:3003001	CfxA	Perfect	ARO:0000008,ARO:3004001,ARO:3004004,ARO:3004014,ARO:3009106	cefoxitin,cefmetazole,cefotetan,flomoxef,second-generation cephalosporin	ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007	beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic
CFXA2	244	276	CAU6DANXX170407:3:1114:8699:80069/1	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	0.999999999999998	100.0	33	72.0	5.82e-18	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
CFXA2	142	173	CAU6DANXX170407:3:1114:8699:80069/2	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	0.9999999999999812	100.0	32	63.2	9.69e-15	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
CFXA2	6	38	CAU6DANXX170407:3:1115:8843:53419/2	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	0.999999999999576	100.0	33	63.9	5.11e-15	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
KLEBSIELLA_PNEUMONIAE_OMPK36	122	144	NC_007779.1_2315251_2315724_2:0:0_1:0:0_49f/1	beta-lactam	YP_005228001.1|FEATURES|Klebsiella_pneumoniae_OmpK36|beta-lactam|Klebsiella_pneumoniae_OmpK36	0.9999995415254888	95.7	23	53.5	1.74e-11	1	ARO:3004122	Klebsiella pneumoniae OmpK37	Loose	ARO:0000004,ARO:0000008,ARO:0000020,ARO:0000032,ARO:3000008,ARO:3000645	monobactam,cefoxitin,carbapenem,cephalosporin,penicillin beta-lactam,cefotaxime	ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007,ARO:3000007	beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,beta-lactam antibiotic
UGD	243	275	CAU6DANXX170407:3:1108:6304:41482/1	peptide	AAC75089.1|FEATURES|ugd|peptide|ugd	0.9999998535728202	87.9	33	67.0	4.72e-16	1	ARO:3003577	ugd	Perfect	ARO:3000454	polymyxin B	ARO:3000053	peptide antibiotic
CLASS_A	54	86	CAU6DANXX170407:3:1105:14702:15315/2	beta-lactam	gi:1045851695:ref:WP_065538049.1:|FEATURES|class_A|beta-lactam|class_A	0.9999999999997856	93.9	33	65.9	8.85e-16	1	ARO:3006225	CepA-44	Loose	ARO:0000032	cephalosporin	ARO:3000007	beta-lactam antibiotic
CLASS_A	91	123	CAU6DANXX170407:3:1105:14702:15315/1	beta-lactam	gi:1045851695:ref:WP_065538049.1:|FEATURES|class_A|beta-lactam|class_A	0.9999999999999616	100.0	33	70.5	1.76e-17	1	ARO:3006225	CepA-44	Loose	ARO:0000032	cephalosporin	ARO:3000007	beta-lactam antibiotic
EVGS	925	963	CAU6DANXX170407:3:1104:9491:87164/1	multidrug	AAC75429.1|FEATURES|evgS|multidrug|evgS	0.9999997299327452	92.3	39	68.9	1.36e-16	1	ARO:3000833	evgS	Perfect	ARO:0000006,ARO:0000011,ARO:0000051,ARO:0000056,ARO:3000662	erythromycin,cloxacillin,tetracycline,oxacillin,norfloxacin	ARO:0000000,ARO:0000001,ARO:3000007,ARO:3000007,ARO:3000050	macrolide antibiotic,fluoroquinolone antibiotic,beta-lactam antibiotic,beta-lactam antibiotic,tetracycline antibiotic
VANS	316	348	CAU6DANXX170407:3:1112:7060:4117/2	glycopeptide	ZP_03233797|FEATURES|vanS|glycopeptide|vanS	1.0	84.8	33	57.0	1.67e-12	1	ARO:3002931	vanS gene in vanA cluster	Loose	ARO:0000028,ARO:0000029	vancomycin,teicoplanin	ARO:3000081,ARO:3000081	glycopeptide antibiotic,glycopeptide antibiotic
TETQ	588	620	CAU6DANXX170407:3:1102:2138:2240/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999994912	100.0	33	74.7	9.6e-19	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETX	336	368	CAU6DANXX170407:3:1116:17442:45308/2	tetracycline	gi:1004700911:gb:AMP49531.1:|FEATURES|tetX|tetracycline|tetX	1.0	100.0	33	65.5	1.65e-15	1	ARO:3000205	tet(X)	Strict	ARO:0000030,ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tigecycline,tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
CFXA2	85	123	CAU6DANXX170407:3:1116:5651:87079/1	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	1.0	100.0	39	85.1	1.09e-22	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
TETQ	449	507	CAU6DANXX170407:3:1103:11471:13724/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	1.0	100.0	59	125.0	4.7200000000000004e-36	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
RPOB2	426	458	CAU6DANXX170407:3:1111:2261:81317/1	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.9999987797753755	84.8	33	58.9	3.45e-13	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
TETQ	242	274	CAU6DANXX170407:3:1101:5603:63878/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999945512	100.0	33	66.6	6.73e-16	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
RPOB2	426	458	CAU6DANXX170407:3:1107:10822:41249/1	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.999998744252828	81.8	33	58.2	6.45e-13	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
TETQ	156	188	CAU6DANXX170407:3:1101:5603:63878/2	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999959934	100.0	33	68.9	1.03e-16	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
ROSA	291	324	CAU6DANXX170407:3:1105:10262:24978/1	fosmidomycin	ZP_04623896|FEATURES|rosA|fosmidomycin|rosA	0.9999999999683687	85.3	34	61.6	4.03e-14	1	ARO:3003048	rosA	Loose	ARO:3000625,ARO:3000626,ARO:3000627,ARO:3000628	polymyxin B1,polymyxin B2,polymyxin B3,polymyxin B4	ARO:3000053,ARO:3000053,ARO:3000053,ARO:3000053	peptide antibiotic,peptide antibiotic,peptide antibiotic,peptide antibiotic
RPOB2	579	611	CAU6DANXX170407:3:1103:2998:38847/1	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.999998897312379	81.8	33	61.6	3.87e-14	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
TETQ	284	316	CAU6DANXX170407:3:1103:17433:23145/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999952612	100.0	33	66.6	6.73e-16	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
RPOB2	355	400	CAU6DANXX170407:3:1106:16171:66260/1	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.999999315201981	80.4	46	79.0	8.34e-20	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
TETQ	104	145	CAU6DANXX170407:3:1112:6977:28934/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.999999999999799	100.0	42	79.0	4.9e-20	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETX	311	343	CAU6DANXX170407:3:1111:9870:54146/1	tetracycline	gi:1004700911:gb:AMP49531.1:|FEATURES|tetX|tetracycline|tetX	1.0	100.0	33	65.5	1.65e-15	1	ARO:3000205	tet(X)	Strict	ARO:0000030,ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tigecycline,tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETX	344	376	CAU6DANXX170407:3:1111:9870:54146/2	tetracycline	gi:1004700911:gb:AMP49531.1:|FEATURES|tetX|tetracycline|tetX	1.0	100.0	33	66.6	6.38e-16	1	ARO:3000205	tet(X)	Strict	ARO:0000030,ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tigecycline,tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
ERMG	63	95	CAU6DANXX170407:3:1102:6234:91674/1	MLS	M15332.gene.p01|FEATURES|ermG|MLS|ermG	0.9999999993215722	100.0	33	74.7	2.65e-19	1	ARO:3000522	ErmG	Strict	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	erythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic
ERMG	114	146	CAU6DANXX170407:3:1102:6234:91674/2	MLS	AAC37034|FEATURES|ermG|MLS|ermG	0.9999999941820874	100.0	33	61.2	3.11e-14	1	ARO:3000522	ErmG	Perfect	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	erythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic
MDTF	483	536	CAU6DANXX170407:3:1116:12771:99205/1	multidrug	gi:803469184:ref:WP_046072900.1:|FEATURES|mdtF|multidrug|mdtF	0.9999999997746044	100.0	54	110.0	6.45e-31	1	ARO:3000796	mdtF	Strict	ARO:0000006,ARO:0000011,ARO:0000056,ARO:3000662	erythromycin,cloxacillin,oxacillin,norfloxacin	ARO:0000000,ARO:0000001,ARO:3000007,ARO:3000007	macrolide antibiotic,fluoroquinolone antibiotic,beta-lactam antibiotic,beta-lactam antibiotic
VANS	324	355	CAU6DANXX170407:3:1108:16226:13871/1	glycopeptide	CAB61230|FEATURES|vanS|glycopeptide|vanS	1.0	87.5	32	57.0	1.67e-12	1	ARO:3002931	vanS gene in vanA cluster	Loose	ARO:0000028,ARO:0000029	vancomycin,teicoplanin	ARO:3000081,ARO:3000081	glycopeptide antibiotic,glycopeptide antibiotic
RPOB2	1031	1061	CAU6DANXX170407:3:1104:7401:68448/2	multidrug	BAD59497.1|FEATURES|rpo
..
0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic
EMRE	60	92	CAU6DANXX170407:3:1113:18090:71525/1	multidrug	ZP_03048536|FEATURES|emrE|multidrug|emrE	0.9999999834234548	100.0	33	70.5	8.25e-19	1	ARO:3004039	Escherichia coli emrE	Strict	ARO:0000006	erythromycin	ARO:0000000	macrolide antibiotic
EMRE	18	50	CAU6DANXX170407:3:1113:18090:71525/2	multidrug	ZP_03048536|FEATURES|emrE|multidrug|emrE	0.999999988681847	100.0	33	75.1	1.25e-20	1	ARO:3004039	Escherichia coli emrE	Strict	ARO:0000006	erythromycin	ARO:0000000	macrolide antibiotic
TETQ	407	439	CAU6DANXX170407:3:1102:1942:64462/2	tetracycline	Z21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ	0.9999999999969242	100.0	33	67.0	4.92e-16	1	ARO:3000191	tet(Q)	Perfect	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETQ	568	600	CAU6DANXX170407:3:1102:1942:64462/1	tetracycline	Z21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ	0.999999999999316	100.0	33	73.6	2.45e-18	1	ARO:3000191	tet(Q)	Perfect	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETX	229	260	CAU6DANXX170407:3:1101:7280:93090/1	tetracycline	gi:1004700911:gb:AMP49531.1:|FEATURES|tetX|tetracycline|tetX	1.0	100.0	32	73.6	2.1e-18	1	ARO:3000205	tet(X)	Strict	ARO:0000030,ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tigecycline,tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
EMRY	212	234	CAU6DANXX170407:3:1104:6368:10645/1	tetracycline	BAA11237.1|FEATURES|emrY|tetracycline|emrY	0.9999999789500456	100.0	23	52.4	4.62e-11	1	ARO:3000254	emrY	Perfect	ARO:0000051	tetracycline	ARO:3000050	tetracycline antibiotic
ERMG	73	105	CAU6DANXX170407:3:1112:14017:27121/1	MLS	M15332.gene.p01|FEATURES|ermG|MLS|ermG	0.9999999993920998	100.0	33	75.5	1.35e-19	1	ARO:3000522	ErmG	Strict	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	erythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic
ERMG	27	59	CAU6DANXX170407:3:1112:14017:27121/2	MLS	M15332.gene.p01|FEATURES|ermG|MLS|ermG	1.0	100.0	33	71.2	5.45e-18	1	ARO:3000522	ErmG	Strict	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	erythromycin,roxithromycin,lincomycin,telithromycin,clarithromycin,clindamycin,tylosin,spiramycin,azithromycin,dirithromycin,pristinamycin IA,quinupristin,virginiamycin M1,madumycin II,griseoviridin,dalfopristin,pristinamycin IB,virginiamycin S2,pristinamycin IC,vernamycin C,patricin A,patricin B,ostreogrycin B3,oleandomycin	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,macrolide antibiotic,lincosamide antibiotic,lincosamide antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic,streptogramin antibiotic
ACRD	918	947	CAU6DANXX170407:3:1116:8853:33330/1	aminoglycoside	YP_490697.1|FEATURES|acrD|aminoglycoside|acrD	0.9999943839450588	80.0	30	52.4	7.05e-11	1	ARO:3000491	acrD	Perfect	ARO:0000005,ARO:0000013,ARO:0000049,ARO:0000052,ARO:3007382	neomycin,amikacin,kanamycin A,tobramycin,gentamicin	ARO:0000016,ARO:0000016,ARO:0000016,ARO:0000016,ARO:0000016	aminoglycoside antibiotic,aminoglycoside antibiotic,aminoglycoside antibiotic,aminoglycoside antibiotic,aminoglycoside antibiotic
CFXA2	235	283	CAU6DANXX170407:3:1101:14288:80257/1	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	1.0	100.0	49	103.0	2.5000000000000002e-29	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
CFXA2	46	95	CAU6DANXX170407:3:1111:7120:98948/1	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	1.0	100.0	50	100.0	1.9699999999999999e-28	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
TETQ	245	277	CAU6DANXX170407:3:1108:4015:12457/2	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999958968	100.0	33	67.8	2.64e-16	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETQ	414	463	CAU6DANXX170407:3:1101:8698:42027/1	tetracycline	Z21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ	0.9999999999999992	98.0	50	101.0	6.87e-28	1	ARO:3000191	tet(Q)	Perfect	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETQ	50	82	CAU6DANXX170407:3:1101:15278:42991/1	tetracycline	Z21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ	0.9999999999999992	100.0	33	67.4	3.6e-16	1	ARO:3000191	tet(Q)	Perfect	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
MDTF	706	738	CAU6DANXX170407:3:1110:11708:72056/2	multidrug	gi:445947058:ref:WP_000024913.1:|FEATURES|mdtF|multidrug|mdtF	0.9999999444726364	100.0	33	69.7	5.5e-17	1	ARO:3000796	mdtF	Strict	ARO:0000006,ARO:0000011,ARO:0000056,ARO:3000662	erythromycin,cloxacillin,oxacillin,norfloxacin	ARO:0000000,ARO:0000001,ARO:3000007,ARO:3000007	macrolide antibiotic,fluoroquinolone antibiotic,beta-lactam antibiotic,beta-lactam antibiotic
MDTF	580	612	CAU6DANXX170407:3:1110:11708:72056/1	multidrug	gi:803469184:ref:WP_046072900.1:|FEATURES|mdtF|multidrug|mdtF	0.9999999915600344	100.0	33	67.0	4.89e-16	1	ARO:3000796	mdtF	Strict	ARO:0000006,ARO:0000011,ARO:0000056,ARO:3000662	erythromycin,cloxacillin,oxacillin,norfloxacin	ARO:0000000,ARO:0000001,ARO:3000007,ARO:3000007	macrolide antibiotic,fluoroquinolone antibiotic,beta-lactam antibiotic,beta-lactam antibiotic
MDTO	279	301	NC_007779.1_4305655_4306126_0:0:0_0:0:0_317/1	multidrug	gi:323171508:gb:EFZ57154.1:|FEATURES|mdtO|multidrug|mdtO	0.9999999998287976	100.0	23	55.1	4.89e-12	1	ARO:3003549	mdtO	Strict	ARO:0000045,ARO:0000047	acriflavine,puromycin	ARO:3000034,ARO:3005386	nucleoside antibiotic,disinfecting agents and antiseptics
DFRF	34	66	CAU6DANXX170407:3:1108:20945:15141/1	diaminopyrimidine	AAD01868.1|FEATURES|dfrF|diaminopyrimidine|dfrF	0.9999387854535118	100.0	33	70.1	4e-18	1	ARO:3002867	dfrF	Perfect	ARO:3000188	trimethoprim	ARO:3000171	diaminopyrimidine antibiotic
DFRF	66	98	CAU6DANXX170407:3:1108:20945:15141/2	diaminopyrimidine	AAD01868.1|FEATURES|dfrF|diaminopyrimidine|dfrF	0.9999283398496522	100.0	33	67.8	3.16e-17	1	ARO:3002867	dfrF	Perfect	ARO:3000188	trimethoprim	ARO:3000171	diaminopyrimidine antibiotic
TETQ	352	384	CAU6DANXX170407:3:1108:4015:12457/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999924536	100.0	33	66.2	9.19e-16	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
BACA	251	281	CAU6DANXX170407:3:1106:8417:75654/1	bacitracin	YP_002937728|FEATURES|bacA|bacitracin|bacA	0.999999999475331	80.6	31	58.9	2.93e-13	1	ARO:3002986	bacA	Loose	ARO:3000629,ARO:3000630,ARO:3000631	bacitracin A,bacitracin B,bacitracin F	ARO:3000053,ARO:3000053,ARO:3000053	peptide antibiotic,peptide antibiotic,peptide antibiotic
CFXA2	218	250	CAU6DANXX170407:3:1109:19851:22298/2	beta-lactam	AF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2	0.9999999999999922	100.0	33	68.2	1.48e-16	1	ARO:3003002	CfxA2	Perfect	ARO:3009106	second-generation cephalosporin	ARO:3000007	beta-lactam antibiotic
RPOB2	804	835	CAU6DANXX170407:3:1104:18231:40035/2	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.999998608464296	84.4	32	55.8	4.21e-12	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
RPOB2	417	464	CAU6DANXX170407:3:1102:7793:63583/1	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.9999994259802474	83.3	48	87.4	6.709999999999999e-23	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
TETQ	422	469	CAU6DANXX170407:3:1103:7711:29479/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999999988	100.0	48	100.0	1.2200000000000002e-27	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
TETQ	323	355	CAU6DANXX170407:3:1102:14130:7410/1	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999982888	100.0	33	72.0	8.52e-18	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
RPOB2	431	465	CAU6DANXX170407:3:1114:10436:19987/1	multidrug	BAD59497.1|FEATURES|rpoB2|multidrug|rpoB2	0.9999990866918076	88.6	35	67.4	4.31e-16	1	ARO:3000501	rpoB2	Perfect	ARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534	rifampin,rifaximin,rifabutin,rifapentine	ARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157	rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic,rifamycin antibiotic
TETQ	240	272	CAU6DANXX170407:3:1102:14130:7410/2	tetracycline	BAD46890|FEATURES|tetQ|tetracycline|tetQ	0.9999999999950568	100.0	33	67.0	4.92e-16	1	ARO:3000191	tet(Q)	Strict	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	tetracycline,doxycycline,minocycline,chlortetracycline,demeclocycline,oxytetracycline	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic,tetracycline antibiotic
MSBA	355	387	CAU6DANXX170407:3:1104:7004:49717/2	nitroimidazole	NP_415434.1|FEATURES|msbA|nitroimidazole|msbA	0.9999289257395336	100.0	33	63.2	1.12e-14	1	ARO:3003950	msbA	Perfect	ARO:3000689	metronidazole	ARO:3004115	nitroimidazole antibiotic
MSBA	275	307	CAU6DANXX170407:3:1104:7004:49717/1	nitroimidazole	NP_415434.1|FEATURES|msbA|nitroimidazole|msbA	0.9998949481248132	100.0	33	59.7	1.87e-13	1	ARO:3003950	msbA	Perfect	ARO:3000689	metronidazole	ARO:3004115	nitroimidazole antibiotic
total 700
-rw-r--r-- 1 1001 1001  22091 Jul 20 09:45 llms-full.txt
-rw-r--r-- 1 1001 1001  12376 Jul 20 09:45 multiqc.log
-rw-r--r-- 1 1001 1001  67892 Jul 20 09:45 multiqc.parquet
-rw-r--r-- 1 1001 1001    124 Jul 20 09:45 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 535987 Jul 20 09:45 multiqc_data.json
-rw-r--r-- 1 1001 1001     85 Jul 20 09:45 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001   1093 Jul 20 09:45 multiqc_section_0_table.txt
-rw-r--r-- 1 1001 1001  16011 Jul 20 09:45 multiqc_section_1_table.txt
-rw-r--r-- 1 1001 1001    186 Jul 20 09:45 multiqc_sources.txt
-rw-r--r-- 1 1001 1001    612 Jul 20 09:45 multiqc_sylphtax.txt
-rw-r--r-- 1 1001 1001     54 Jul 20 09:45 sylphtax-top-n-plot_Class.txt
-rw-r--r-- 1 1001 1001     43 Jul 20 09:45 sylphtax-top-n-plot_Domain.txt
-rw-r--r-- 1 1001 1001     53 Jul 20 09:45 sylphtax-top-n-plot_Family.txt
-rw-r--r-- 1 1001 1001     46 Jul 20 09:45 sylphtax-top-n-plot_Genus.txt
-rw-r--r-- 1 1001 1001     51 Jul 20 09:45 sylphtax-top-n-plot_Order.txt
-rw-r--r-- 1 1001 1001     49 Jul 20 09:45 sylphtax-top-n-plot_Phylum.txt
-rw-r--r-- 1 1001 1001     55 Jul 20 09:45 sylphtax-top-n-plot_Species.txt
-rw-r--r-- 1 1001 1001     56 Jul 20 09:45 sylphtax-top-n-plot_Strain.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bb574152841e11f18ae06045bd4a52bb"`
chromInfo	`"/tmp/tmpra7ms2y_/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__": 55, "description": null, "input": {"values": [{"id": 25, "src": "hdca"}]}, "plot_type": "table", "section_name": "ARGs detected by Groot and normalized with argNorm", "software": "custom_content", "title": null, "xlab": null, "ylab": null}}, {"__index__": 1, "software_cond": {"__current_case__": 55, "description": null, "input": {"values": [{"id": 18, "src": "hdca"}]}, "plot_type": "table", "section_name": "ARGs detected by DeepARG", "software": "custom_content", "title": null, "xlab": null, "ylab": null}}, {"__index__": 2, "software_cond": {"__current_case__": 30, "input": {"values": [{"id": 21, "src": "hdca"}]}, "software": "sylphtax"}}]
title	`""`

Other invocation details
- history_id
  - 56c0b8ee7331d2e6
- history_state
  - ok
- invocation_id
  - 56c0b8ee7331d2e6
- invocation_state
  - scheduled
- workflow_id
  - 56c0b8ee7331d2e6

Updating workflows/microbiome/metagenomic-raw-reads-amr-analysis from…

abd73e7

… 1.2 to 1.3

gxydevbot requested a review from hugolefeuvre as a code owner July 20, 2026 09:04

hugolefeuvre added 2 commits July 20, 2026 11:27

Update release version to 1.2.1

9707e58

Change version from 1.3 to 1.2.1 in CHANGELOG.md

17072ae

Updated version number and date for the changelog.

hugolefeuvre approved these changes Jul 20, 2026

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Updating workflows/microbiome/metagenomic-raw-reads-amr-analysis from 1.2 to 1.3 - #1314

Updating workflows/microbiome/metagenomic-raw-reads-amr-analysis from 1.2 to 1.3#1314
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