Metagenomic raw reads analysis workflow without assembly #1014

hugolefeuvre · 2025-11-03T14:36:12Z

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

hugolefeuvre · 2025-11-03T14:44:07Z

They are missing DBs on cvmfs (Sylph, Groot and DeepARG) so tests will fail but I ask IDC to added DBs : galaxyproject/idc#77

github-actions · 2025-11-03T14:46:45Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 16 requires a dataset collection created by step 13, but dataset collection entered a failed state.

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	{"__current_case__": 0, "input_param": "arg-annot.90-1.1.2-09122024", "mappings": [{"__index__": 0, "from": "arg-annot.90-1.1.2-09122024", "to": "groot-argannot"}, {"__index__": 1, "from": "card (90 percent identity)", "to": "groot-card"}, {"__index__": 2, "from": "groot-core-db (90 percent identity)", "to": "groot-core-db"}, {"__index__": 3, "from": "resfinder (90 percent identity)", "to": "groot-resfinder"}, {"__index__": 4, "from": "groot-db (90 percent identity)", "to": "groot-db"}], "type": "text"}
output_param_type	`"text"`
unmapped	`{"__current_case__": 1, "on_unmapped": "fail"}`

Step 12: 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 error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-03072025"`
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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_21072025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_21072025"}`
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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpozvmlccj/files/6/8/5/dataset_6857f6bd-be7a-40a6-be93-5230ab2606bc.dat' sanger.gz '/tmp/tmpozvmlccj/files/d/2/6/dataset_d2602e61-033b-4dd3-bd1d-535391126046.dat' sanger.gz '/tmp/tmpozvmlccj/job_working_directory/000/8/outputs/dataset_6c55de04-ceca-4944-942f-4bb19b321b89.dat' '/tmp/tmpozvmlccj/job_working_directory/000/8/outputs/dataset_e37bb5ff-a365-4247-9657-9ff9242f6e60.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-09122024", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: Unlabelled step:
- step_state: new
Step 20: Unlabelled step:
- step_state: new
Step 3: Select a Groot database:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 5: Select a Sylph database:
- step_state: scheduled
Step 6: Select a Sylph tax database:
- step_state: scheduled
Step 7: Groot average base pair length of reads:
- step_state: scheduled
Step 8: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpozvmlccj/job_working_directory/000/3/outputs/dataset_301ac29e-616d-48da-800e-ecf01bf67b21.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpozvmlccj/job_working_directory/000/3/outputs/dataset_301ac29e-616d-48da-800e-ecf01bf67b21.dat';

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/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: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "be6195f4b8c311f082707ced8d0a0a79"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - f8affb27b52afdab
- history_state
  - new
- invocation_id
  - f8affb27b52afdab
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 12, 'hdca_id': 'f9b1b179fbb2dfa1', 'reason': 'collection_failed', 'workflow_step_id': 15}]
- workflow_id
  - f8affb27b52afdab

github-actions · 2025-11-11T12:20:53Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

Upload job [590e8452f07b35d7] produced output [1: PSM6XBT3_500k_R1.fastq.gz] in state [error]

github-actions · 2025-11-12T13:01:34Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "83c5d47cbfbd11f0bb736045bd8384a1"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp0xmsn2s3/files/7/c/6/dataset_7c642f47-35fd-4214-a3a7-e084b84017a7.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp0xmsn2s3/files/4/b/d/dataset_4bdf702a-9578-497b-b8ec-f5b805daf349.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: 125000 Both Surviving: 125000 (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%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  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 = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 244169.33reads/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 [00:07,  7.44s/chunks]
1chunks [00:07,  7.44s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 41731.31it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (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__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp0xmsn2s3/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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp0xmsn2s3/files/7/c/6/dataset_7c642f47-35fd-4214-a3a7-e084b84017a7.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp0xmsn2s3/files/4/b/d/dataset_4bdf702a-9578-497b-b8ec-f5b805daf349.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/tmp0xmsn2s3/job_working_directory/000/6/outputs/dataset_2acf163a-57a6-448d-9f05-105ac2f9cb8d.dat'  && cp '/tmp/tmp0xmsn2s3/job_working_directory/000/6/configs/tmpmsrpgsbe' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp0xmsn2s3/job_working_directory/000/6/outputs/dataset_2acf163a-57a6-448d-9f05-105ac2f9cb8d.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-12T11:49:06.567Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-12T11:49:06.768Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-12T11:49:06.768Z INFO  [sylph::sketch] Finished.
2025-11-12T11:49:06.771Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmp0xmsn2s3/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp0xmsn2s3/job_working_directory/000/6/outputs/dataset_2acf163a-57a6-448d-9f05-105ac2f9cb8d.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp0xmsn2s3/files/7/c/6/dataset_7c642f47-35fd-4214-a3a7-e084b84017a7.dat' sanger.gz '/tmp/tmp0xmsn2s3/files/4/b/d/dataset_4bdf702a-9578-497b-b8ec-f5b805daf349.dat' sanger.gz '/tmp/tmp0xmsn2s3/job_working_directory/000/7/outputs/dataset_a453d95c-839d-494e-bb94-f0843a8b98e7.dat' '/tmp/tmp0xmsn2s3/job_working_directory/000/7/outputs/dataset_615e273f-3da9-4c8c-9869-2db69e725879.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp0xmsn2s3/files/6/c/3/dataset_6c33f76d-ab25-4bdd-85c6-1e53e1ee4dfb.dat' -o '/tmp/tmp0xmsn2s3/job_working_directory/000/8/outputs/dataset_bb7e74db-579b-4f15-ab6b-39b92cf5deda.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp0xmsn2s3/job_working_directory/000/8/outputs/dataset_bb7e74db-579b-4f15-ab6b-39b92cf5deda.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp0xmsn2s3/files/a/4/5/dataset_a453d95c-839d-494e-bb94-f0843a8b98e7.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/tmp0xmsn2s3/job_working_directory/000/9/outputs/dataset_afc6aebe-aa71-45b3-b777-794d601d6a8b.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp0xmsn2s3/files/a/4/5/dataset_a453d95c-839d-494e-bb94-f0843a8b98e7.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__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp0xmsn2s3/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0xmsn2s3/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp0xmsn2s3/files/b/b/7/dataset_bb7e74db-579b-4f15-ab6b-39b92cf5deda.dat' '/tmp/tmp0xmsn2s3/job_working_directory/000/10/outputs/dataset_3fa7d410-8b10-47ca-953a-dabf67ec2a0f.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "83c5d47cbfbd11f0bb736045bd8384a1"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp0xmsn2s3/files/a/f/c/dataset_afc6aebe-aa71-45b3-b777-794d601d6a8b.dat' -o '/tmp/tmp0xmsn2s3/job_working_directory/000/11/outputs/dataset_57feef54-eb18-49df-9da6-c31ac5c4c94f.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp0xmsn2s3/job_working_directory/000/11/outputs/dataset_57feef54-eb18-49df-9da6-c31ac5c4c94f.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "83c5d47cbfbd11f0bb736045bd8384a1"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0xmsn2s3/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp0xmsn2s3/files/5/7/f/dataset_57feef54-eb18-49df-9da6-c31ac5c4c94f.dat' '/tmp/tmp0xmsn2s3/job_working_directory/000/13/outputs/dataset_8b2ec3ba-c23b-41b5-bc60-1dececb0ec88.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp0xmsn2s3/job_working_directory/000/3/outputs/dataset_b803da1d-79a0-4da6-9daf-2ea54fb48497.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp0xmsn2s3/job_working_directory/000/3/outputs/dataset_b803da1d-79a0-4da6-9daf-2ea54fb48497.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/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"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - ed2addef42524e29
- history_state
  - error
- invocation_id
  - ed2addef42524e29
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - ed2addef42524e29

hugolefeuvre · 2025-11-12T13:46:24Z

Hi, it seems that the tests fail for sylph job due to memory issue, do you know how to handle this ?

❌ Failed job f08065326a26f9cc:
Tool ID:
toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0
Exit code: 137

github-actions · 2025-11-14T11:57:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

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

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cc2b60fec14a11f0a059000d3a047ab5"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp9yfvh3ca/files/9/d/d/dataset_9ddb3a13-517f-4f52-9e9f-ebb128586c72.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp9yfvh3ca/files/b/b/f/dataset_bbf1e905-17ae-4d59-803c-c30b96c6bb09.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: 125000 Both Surviving: 125000 (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%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  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 = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 256164.41reads/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 [00:07,  7.95s/chunks]
1chunks [00:07,  7.95s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 40366.95it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (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__	`"cc2b60fec14a11f0a059000d3a047ab5"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp9yfvh3ca/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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp9yfvh3ca/files/9/d/d/dataset_9ddb3a13-517f-4f52-9e9f-ebb128586c72.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp9yfvh3ca/files/b/b/f/dataset_bbf1e905-17ae-4d59-803c-c30b96c6bb09.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/tmp9yfvh3ca/job_working_directory/000/6/outputs/dataset_84f682e3-66cc-4a3d-a9a2-494762ae71cd.dat'  && cp '/tmp/tmp9yfvh3ca/job_working_directory/000/6/configs/tmpx61m__8i' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp9yfvh3ca/job_working_directory/000/6/outputs/dataset_84f682e3-66cc-4a3d-a9a2-494762ae71cd.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-14T11:12:57.423Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-14T11:12:57.671Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-14T11:12:57.671Z INFO  [sylph::sketch] Finished.
2025-11-14T11:12:57.674Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmp9yfvh3ca/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp9yfvh3ca/job_working_directory/000/6/outputs/dataset_84f682e3-66cc-4a3d-a9a2-494762ae71cd.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp9yfvh3ca/files/9/d/d/dataset_9ddb3a13-517f-4f52-9e9f-ebb128586c72.dat' sanger.gz '/tmp/tmp9yfvh3ca/files/b/b/f/dataset_bbf1e905-17ae-4d59-803c-c30b96c6bb09.dat' sanger.gz '/tmp/tmp9yfvh3ca/job_working_directory/000/7/outputs/dataset_1eba606f-714f-46d8-9950-ea159ac4921e.dat' '/tmp/tmp9yfvh3ca/job_working_directory/000/7/outputs/dataset_50fadc42-800e-434b-b1e5-09451cdb5c8f.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp9yfvh3ca/files/6/f/8/dataset_6f898eb6-8bd6-4c34-bdbf-e3a5b8ecfc5f.dat' -o '/tmp/tmp9yfvh3ca/job_working_directory/000/8/outputs/dataset_a511072b-5819-47eb-b7a6-12a8bc150d55.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp9yfvh3ca/job_working_directory/000/8/outputs/dataset_a511072b-5819-47eb-b7a6-12a8bc150d55.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp9yfvh3ca/files/1/e/b/dataset_1eba606f-714f-46d8-9950-ea159ac4921e.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/tmp9yfvh3ca/job_working_directory/000/9/outputs/dataset_21aaf928-50e7-46a0-ada4-7cdc0552aa46.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp9yfvh3ca/files/1/e/b/dataset_1eba606f-714f-46d8-9950-ea159ac4921e.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 report --covCutoff 0.6
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp9yfvh3ca/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9yfvh3ca/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp9yfvh3ca/files/a/5/1/dataset_a511072b-5819-47eb-b7a6-12a8bc150d55.dat' '/tmp/tmp9yfvh3ca/job_working_directory/000/10/outputs/dataset_a4864616-c481-4a50-aa7f-b245f835df8d.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cc2b60fec14a11f0a059000d3a047ab5"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp9yfvh3ca/files/2/1/a/dataset_21aaf928-50e7-46a0-ada4-7cdc0552aa46.dat' -o '/tmp/tmp9yfvh3ca/job_working_directory/000/11/outputs/dataset_57d1adf9-2f20-4a57-9f3d-91dc646f0c20.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp9yfvh3ca/job_working_directory/000/11/outputs/dataset_57d1adf9-2f20-4a57-9f3d-91dc646f0c20.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cc2b60fec14a11f0a059000d3a047ab5"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9yfvh3ca/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp9yfvh3ca/files/5/7/d/dataset_57d1adf9-2f20-4a57-9f3d-91dc646f0c20.dat' '/tmp/tmp9yfvh3ca/job_working_directory/000/13/outputs/dataset_ce579c47-318c-471b-a9cb-5e4f1ccfcc33.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp9yfvh3ca/job_working_directory/000/3/outputs/dataset_46005000-7bc0-41ee-84a3-6ff899fc552d.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp9yfvh3ca/job_working_directory/000/3/outputs/dataset_46005000-7bc0-41ee-84a3-6ff899fc552d.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/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"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - d9e28052d9b695ad
- history_state
  - error
- invocation_id
  - d9e28052d9b695ad
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - d9e28052d9b695ad

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4f3069aac14a11f0bb73000d3a9b19b5"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmpbt8i0a4x/files/a/f/3/dataset_af3b10e7-f9b4-42ad-abb0-ec2d9bb64b5c.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmpbt8i0a4x/files/9/1/6/dataset_916217bb-fb2b-4778-bbe0-d35f775d614d.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: 125000 Both Surviving: 125000 (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%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  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 = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 191721.01reads/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,  6.69s/chunks]
1chunks [00:06,  6.69s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 40937.66it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (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__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpbt8i0a4x/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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmpbt8i0a4x/files/a/f/3/dataset_af3b10e7-f9b4-42ad-abb0-ec2d9bb64b5c.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmpbt8i0a4x/files/9/1/6/dataset_916217bb-fb2b-4778-bbe0-d35f775d614d.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/tmpbt8i0a4x/job_working_directory/000/6/outputs/dataset_47fec8bf-206a-4189-a470-68df96ff36fb.dat'  && cp '/tmp/tmpbt8i0a4x/job_working_directory/000/6/configs/tmp8oktn8q_' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmpbt8i0a4x/job_working_directory/000/6/outputs/dataset_47fec8bf-206a-4189-a470-68df96ff36fb.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-14T11:09:25.902Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-14T11:09:26.111Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-14T11:09:26.111Z INFO  [sylph::sketch] Finished.
2025-11-14T11:09:26.115Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmpbt8i0a4x/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpbt8i0a4x/job_working_directory/000/6/outputs/dataset_47fec8bf-206a-4189-a470-68df96ff36fb.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpbt8i0a4x/files/a/f/3/dataset_af3b10e7-f9b4-42ad-abb0-ec2d9bb64b5c.dat' sanger.gz '/tmp/tmpbt8i0a4x/files/9/1/6/dataset_916217bb-fb2b-4778-bbe0-d35f775d614d.dat' sanger.gz '/tmp/tmpbt8i0a4x/job_working_directory/000/7/outputs/dataset_ea71a63e-735f-4cbc-9ea5-2151f141740c.dat' '/tmp/tmpbt8i0a4x/job_working_directory/000/7/outputs/dataset_bd1d60b5-4e07-49b5-a6ed-650b2a4aa2bc.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmpbt8i0a4x/files/7/f/0/dataset_7f0d1552-6100-4768-8965-530e5a7c4cc4.dat' -o '/tmp/tmpbt8i0a4x/job_working_directory/000/8/outputs/dataset_aefe2f72-d6bd-43c7-a350-883ed4ece463.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpbt8i0a4x/job_working_directory/000/8/outputs/dataset_aefe2f72-d6bd-43c7-a350-883ed4ece463.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmpbt8i0a4x/files/e/a/7/dataset_ea71a63e-735f-4cbc-9ea5-2151f141740c.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/tmpbt8i0a4x/job_working_directory/000/9/outputs/dataset_ab951005-147e-4904-9a42-f0f68c819394.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmpbt8i0a4x/files/e/a/7/dataset_ea71a63e-735f-4cbc-9ea5-2151f141740c.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__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpbt8i0a4x/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpbt8i0a4x/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpbt8i0a4x/files/a/e/f/dataset_aefe2f72-d6bd-43c7-a350-883ed4ece463.dat' '/tmp/tmpbt8i0a4x/job_working_directory/000/10/outputs/dataset_d9c5bfb7-689f-4eba-a7fe-b74670413f20.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4f3069aac14a11f0bb73000d3a9b19b5"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmpbt8i0a4x/files/a/b/9/dataset_ab951005-147e-4904-9a42-f0f68c819394.dat' -o '/tmp/tmpbt8i0a4x/job_working_directory/000/11/outputs/dataset_28b60f79-163a-402d-965a-d788a082b941.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpbt8i0a4x/job_working_directory/000/11/outputs/dataset_28b60f79-163a-402d-965a-d788a082b941.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4f3069aac14a11f0bb73000d3a9b19b5"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpbt8i0a4x/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpbt8i0a4x/files/2/8/b/dataset_28b60f79-163a-402d-965a-d788a082b941.dat' '/tmp/tmpbt8i0a4x/job_working_directory/000/13/outputs/dataset_10057fc4-0aed-4086-b1f2-709016bb89c0.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpbt8i0a4x/job_working_directory/000/3/outputs/dataset_222b2830-867b-4047-aaa4-e55eda319933.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpbt8i0a4x/job_working_directory/000/3/outputs/dataset_222b2830-867b-4047-aaa4-e55eda319933.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/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"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 03876b3b6663412d
- history_state
  - error
- invocation_id
  - 03876b3b6663412d
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - 03876b3b6663412d

github-actions · 2025-11-14T14:29:31Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "475bce76c15f11f0bb736045bdd8cbdf"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp8rkid8xk/files/7/3/7/dataset_7370928e-a924-44a8-82c8-67dadcd36e0e.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp8rkid8xk/files/4/2/e/dataset_42e496a6-dcf2-4266-bd7a-b84fa28a4aa5.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: 125000 Both Surviving: 125000 (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%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  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 = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.002s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 150833.01reads/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 [00:07,  7.03s/chunks]
1chunks [00:07,  7.03s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 39418.52it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (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__	`"475bce76c15f11f0bb736045bdd8cbdf"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp8rkid8xk/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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp8rkid8xk/files/7/3/7/dataset_7370928e-a924-44a8-82c8-67dadcd36e0e.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp8rkid8xk/files/4/2/e/dataset_42e496a6-dcf2-4266-bd7a-b84fa28a4aa5.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/tmp8rkid8xk/job_working_directory/000/6/outputs/dataset_1edbdb09-b3c2-42a8-b231-ded47e6a73e8.dat'  && cp '/tmp/tmp8rkid8xk/job_working_directory/000/6/configs/tmpao47u0nb' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp8rkid8xk/job_working_directory/000/6/outputs/dataset_1edbdb09-b3c2-42a8-b231-ded47e6a73e8.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-14T13:39:28.114Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-14T13:39:28.372Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-14T13:39:28.373Z INFO  [sylph::sketch] Finished.
2025-11-14T13:39:28.376Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmp8rkid8xk/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp8rkid8xk/job_working_directory/000/6/outputs/dataset_1edbdb09-b3c2-42a8-b231-ded47e6a73e8.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp8rkid8xk/files/7/3/7/dataset_7370928e-a924-44a8-82c8-67dadcd36e0e.dat' sanger.gz '/tmp/tmp8rkid8xk/files/4/2/e/dataset_42e496a6-dcf2-4266-bd7a-b84fa28a4aa5.dat' sanger.gz '/tmp/tmp8rkid8xk/job_working_directory/000/7/outputs/dataset_3e04cf60-cc89-4c00-b2f1-2da00f285000.dat' '/tmp/tmp8rkid8xk/job_working_directory/000/7/outputs/dataset_0c9191e9-a25a-4b4d-aa7a-088b4a18e486.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp8rkid8xk/files/c/0/e/dataset_c0ec7c2b-15b6-48af-b46c-338d13e0ad0c.dat' -o '/tmp/tmp8rkid8xk/job_working_directory/000/8/outputs/dataset_e7e6f307-15f5-4140-9477-0d08b8ad21ff.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp8rkid8xk/job_working_directory/000/8/outputs/dataset_e7e6f307-15f5-4140-9477-0d08b8ad21ff.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp8rkid8xk/files/3/e/0/dataset_3e04cf60-cc89-4c00-b2f1-2da00f285000.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/tmp8rkid8xk/job_working_directory/000/9/outputs/dataset_54ec7632-5d12-4a18-ad8b-003741dfa87f.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp8rkid8xk/files/3/e/0/dataset_3e04cf60-cc89-4c00-b2f1-2da00f285000.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__	`"475bce76c15f11f0bb736045bdd8cbdf"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp8rkid8xk/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8rkid8xk/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp8rkid8xk/files/e/7/e/dataset_e7e6f307-15f5-4140-9477-0d08b8ad21ff.dat' '/tmp/tmp8rkid8xk/job_working_directory/000/10/outputs/dataset_38c1b188-a607-4fcb-b187-91436870eaa9.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "475bce76c15f11f0bb736045bdd8cbdf"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp8rkid8xk/files/5/4/e/dataset_54ec7632-5d12-4a18-ad8b-003741dfa87f.dat' -o '/tmp/tmp8rkid8xk/job_working_directory/000/11/outputs/dataset_dd7ba87e-de6b-4cbd-bf59-8199800ff672.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp8rkid8xk/job_working_directory/000/11/outputs/dataset_dd7ba87e-de6b-4cbd-bf59-8199800ff672.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "475bce76c15f11f0bb736045bdd8cbdf"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8rkid8xk/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp8rkid8xk/files/d/d/7/dataset_dd7ba87e-de6b-4cbd-bf59-8199800ff672.dat' '/tmp/tmp8rkid8xk/job_working_directory/000/13/outputs/dataset_07b8bf66-b5fa-4c4a-aaed-5d63119dc497.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp8rkid8xk/job_working_directory/000/3/outputs/dataset_d5ef1f59-618d-4237-ae51-58f3ae3418ed.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp8rkid8xk/job_working_directory/000/3/outputs/dataset_d5ef1f59-618d-4237-ae51-58f3ae3418ed.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/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"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 5c0d57b126876b4e
- history_state
  - error
- invocation_id
  - 5c0d57b126876b4e
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - 5c0d57b126876b4e

github-actions · 2025-11-20T10:41:03Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '14' (DeepARG database) is not optional and no input provided.","err_code":0}

github-actions · 2025-11-20T10:41:07Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '14' (DeepARG database) is not optional and no input provided.","err_code":0}

github-actions · 2025-11-20T10:59:50Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "42526208c5fd11f0a0597c1e52d6ad2f"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmplsda32zq/files/f/e/a/dataset_fea4ac36-2d86-44c2-83f9-004ca2267419.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmplsda32zq/files/d/2/9/dataset_d29baef3-acb8-4dc1-b394-179226d33977.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: 125000 Both Surviving: 125000 (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%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  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 = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 215168.33reads/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 [00:07,  7.25s/chunks]
1chunks [00:07,  7.25s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 34214.57it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (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__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmplsda32zq/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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmplsda32zq/files/f/e/a/dataset_fea4ac36-2d86-44c2-83f9-004ca2267419.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmplsda32zq/files/d/2/9/dataset_d29baef3-acb8-4dc1-b394-179226d33977.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/tmplsda32zq/job_working_directory/000/6/outputs/dataset_5b3f4272-1593-4997-8036-a9ebc7531e6a.dat'  && cp '/tmp/tmplsda32zq/job_working_directory/000/6/configs/tmp55m8tqk5' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmplsda32zq/job_working_directory/000/6/outputs/dataset_5b3f4272-1593-4997-8036-a9ebc7531e6a.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-20T10:40:35.319Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-20T10:40:35.570Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-20T10:40:35.570Z INFO  [sylph::sketch] Finished.
2025-11-20T10:40:35.574Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmplsda32zq/job_working_directory/000/6/tool_script.sh: line 23:    11 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmplsda32zq/job_working_directory/000/6/outputs/dataset_5b3f4272-1593-4997-8036-a9ebc7531e6a.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmplsda32zq/files/f/e/a/dataset_fea4ac36-2d86-44c2-83f9-004ca2267419.dat' sanger.gz '/tmp/tmplsda32zq/files/d/2/9/dataset_d29baef3-acb8-4dc1-b394-179226d33977.dat' sanger.gz '/tmp/tmplsda32zq/job_working_directory/000/7/outputs/dataset_36dff02b-724c-4f74-9098-69d14f9ae0bd.dat' '/tmp/tmplsda32zq/job_working_directory/000/7/outputs/dataset_7d9553c7-f839-41d2-94d8-4e193d170c3f.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm DeepARG:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmplsda32zq/files/0/0/b/dataset_00b65ad5-1c6b-436b-9465-76c9ddf2fe97.dat' -o '/tmp/tmplsda32zq/job_working_directory/000/8/outputs/dataset_6e32be25-e54c-4484-97c6-cf7ac7eef485.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmplsda32zq/job_working_directory/000/8/outputs/dataset_6e32be25-e54c-4484-97c6-cf7ac7eef485.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmplsda32zq/files/3/6/d/dataset_36dff02b-724c-4f74-9098-69d14f9ae0bd.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/tmplsda32zq/job_working_directory/000/9/outputs/dataset_5a6abb09-d7ba-4b1a-8717-150289de2cda.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmplsda32zq/files/3/6/d/dataset_36dff02b-724c-4f74-9098-69d14f9ae0bd.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__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmplsda32zq/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmplsda32zq/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmplsda32zq/files/6/e/3/dataset_6e32be25-e54c-4484-97c6-cf7ac7eef485.dat' '/tmp/tmplsda32zq/job_working_directory/000/10/outputs/dataset_364885ba-3456-40fb-b612-58fe1d3eea13.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "42526208c5fd11f0a0597c1e52d6ad2f"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: argNorm Groot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmplsda32zq/files/5/a/6/dataset_5a6abb09-d7ba-4b1a-8717-150289de2cda.dat' -o '/tmp/tmplsda32zq/job_working_directory/000/11/outputs/dataset_6d5fefa3-0dbd-431d-a931-eb4079ec007e.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmplsda32zq/job_working_directory/000/11/outputs/dataset_6d5fefa3-0dbd-431d-a931-eb4079ec007e.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "42526208c5fd11f0a0597c1e52d6ad2f"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmplsda32zq/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmplsda32zq/files/6/d/5/dataset_6d5fefa3-0dbd-431d-a931-eb4079ec007e.dat' '/tmp/tmplsda32zq/job_working_directory/000/13/outputs/dataset_fc5f978c-6203-4947-92ea-e3082066d070.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Sylph database:
- step_state: scheduled
Step 7: Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmplsda32zq/job_working_directory/000/3/outputs/dataset_2029e14a-2a14-4963-9c93-c4c183c03665.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmplsda32zq/job_working_directory/000/3/outputs/dataset_2029e14a-2a14-4963-9c93-c4c183c03665.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/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"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 42f676f6b5b014ad
- history_state
  - error
- invocation_id
  - 42f676f6b5b014ad
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - 42f676f6b5b014ad

github-actions · 2025-11-20T11:31:26Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "12631b72c5fe11f0a059000d3ad90467"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmpyfijlz_q/files/0/d/5/dataset_0d5ba683-5616-4337-bd55-868bdbc80712.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmpyfijlz_q/files/a/e/a/dataset_aeacef9a-5046-4c09-a81c-25b0a7f2b29f.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: 125000 Both Surviving: 125000 (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%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  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 = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.002s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 280375.79reads/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 [00:07,  7.17s/chunks]
1chunks [00:07,  7.17s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 35676.11it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (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__	`"12631b72c5fe11f0a059000d3ad90467"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpyfijlz_q/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 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmpyfijlz_q/files/0/d/5/dataset_0d5ba683-5616-4337-bd55-868bdbc80712.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmpyfijlz_q/files/a/e/a/dataset_aeacef9a-5046-4c09-a81c-25b0a7f2b29f.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/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat'  && cp '/tmp/tmpyfijlz_q/job_working_directory/000/6/configs/tmp6_a5o3lt' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-20T10:46:40.540Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-20T10:46:40.739Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-20T10:46:40.740Z INFO  [sylph::sketch] Finished.
2025-11-20T10:46:40.741Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmpyfijlz_q/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpyfijlz_q/files/0/d/5/dataset_0d5ba683-5616-4337-bd55-868bdbc80712.dat' sanger.gz '/tmp/tmpyfijlz_q/files/a/e/a/dataset_aeacef9a-5046-4c09-a81c-25b0a7f2b29f.dat' sanger.gz '/tmp/tmpyfijlz_q/job_working_directory/000/7/outputs/dataset_6ea745cb-9ac0-4b8e-a89f-084f24f8509d.dat' '/tmp/tmpyfijlz_q/job_working_directory/000/7/outputs/dataset_c8e95a59-61e0-4d6c-a30e-e412d800a27d.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm DeepARG:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmpyfijlz_q/files/2/9/7/dataset_2979c4df-fb11-4212-8f0f-526e203170fd.dat' -o '/tmp/tmpyfijlz_q/job_working_directory/000/8/outputs/dataset_25c34d51-4768-41ba-ab95-2979ec877b6d.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpyfijlz_q/job_working_directory/000/8/outputs/dataset_25c34d51-4768-41ba-ab95-2979ec877b6d.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmpyfijlz_q/files/6/e/a/dataset_6ea745cb-9ac0-4b8e-a89f-084f24f8509d.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/tmpyfijlz_q/job_working_directory/000/9/outputs/dataset_a4285cd1-a027-4ec7-a1df-ce270e5879d5.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmpyfijlz_q/files/6/e/a/dataset_6ea745cb-9ac0-4b8e-a89f-084f24f8509d.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__	`"12631b72c5fe11f0a059000d3ad90467"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpyfijlz_q/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpyfijlz_q/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpyfijlz_q/files/2/5/c/dataset_25c34d51-4768-41ba-ab95-2979ec877b6d.dat' '/tmp/tmpyfijlz_q/job_working_directory/000/10/outputs/dataset_ae1e1605-0926-431f-a8c2-e67a4364e376.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "12631b72c5fe11f0a059000d3ad90467"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: argNorm Groot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmpyfijlz_q/files/a/4/2/dataset_a4285cd1-a027-4ec7-a1df-ce270e5879d5.dat' -o '/tmp/tmpyfijlz_q/job_working_directory/000/11/outputs/dataset_5989dcdc-1ebf-479d-8f0a-41e47d76cb27.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpyfijlz_q/job_working_directory/000/11/outputs/dataset_5989dcdc-1ebf-479d-8f0a-41e47d76cb27.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "12631b72c5fe11f0a059000d3ad90467"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpyfijlz_q/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpyfijlz_q/files/5/9/8/dataset_5989dcdc-1ebf-479d-8f0a-41e47d76cb27.dat' '/tmp/tmpyfijlz_q/job_working_directory/000/13/outputs/dataset_c4e8be53-821f-47d4-adf4-5f636971a90f.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Sylph database:
- step_state: scheduled
Step 7: Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpyfijlz_q/job_working_directory/000/3/outputs/dataset_b1d9e435-57fa-40c8-9bfb-b1e557027a48.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpyfijlz_q/job_working_directory/000/3/outputs/dataset_b1d9e435-57fa-40c8-9bfb-b1e557027a48.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/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"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - b2bc19486b170c0c
- history_state
  - error
- invocation_id
  - b2bc19486b170c0c
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - b2bc19486b170c0c

hugolefeuvre · 2025-12-09T15:04:12Z

Hi @mvdbeek, did you have any idea why this tool failed ? In test summary we got this one :
/tmp/tmpyfijlz_q/job_working_directory/000/6/tool_script.sh: line 23: 12 Killed sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat'
And on the log there is this issue that I thought it was linked to the tool consumption but I'm not sure :

❌ Failed job f08065326a26f9cc:
Tool ID:
toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0
Exit code: 137

mvdbeek · 2025-12-09T17:17:32Z

Ran out of memory. I'd check against a live instance how much memory this needs and see if you can optimize anything about the test data ?

hugolefeuvre · 2025-12-09T17:52:32Z

I have this metrics linked to memory that I found on europe instance on a previous test :
Max memory usage recorded 25.3 GB
Memory Allocated (MB) 3891
Did I have to reduce input data ? Or ask for more memory for the tool somewhere in particular ?

mvdbeek · 2025-12-09T19:38:04Z

Can you share the link ? I think allocated and recorded values are probably mixed up ?

hugolefeuvre · 2025-12-10T09:14:47Z

I think allocated and recorded values are probably mixed up ?

Job details for sylph with the same input :
https://usegalaxy.eu/datasets/26c75dcccb616ac8b38139308a51c39b/details

mvdbeek · 2025-12-10T11:52:58Z

You need to share the history when you share links, i can't access these otherwise.

hugolefeuvre · 2025-12-10T13:04:24Z

You need to share the history when you share links, i can't access these otherwise.

Sorry, here is the shared history : https://usegalaxy.eu/u/lefeuvre-h/h/cwl-target-history

mvdbeek · 2025-12-10T14:48:05Z

Memory Allocated (MB) 3891

So this job should have failed because it used more memory than allocated. @bgruening are you not enforcing memory limits ?

For the issue at hand, 25GB memory is too much, the fastq files don't look too large, so I guess the memory consumption is due to the reference database. There's another reference database, do you know if this is any smaller ? You could try running against that one.

hugolefeuvre · 2025-12-10T14:55:30Z

For the issue at hand, 25GB memory is too much, the fastq files don't look too large, so I guess the memory consumption is due to the reference database. There's another reference database, do you know if this is any smaller ? You could try running against that one.

There is smaller database linked to this tool but I need to add them into cvmfs, hope it don't take too much time

hugolefeuvre · 2025-12-10T15:40:25Z

Request on idc : galaxyproject/idc#77
This DB is 800Mo instead of 13Go for the actual one, hope it works.

bebatut · 2025-12-11T14:30:18Z

/review 1014

Copilot

Pull request overview

This PR adds a new workflow for metagenomic analysis from raw reads without assembly, focused on taxonomic profiling and antimicrobial resistance (AMR) detection. The workflow is contributed by the ABRomics consortium and processes paired-end short reads to provide both taxonomic and functional (AMR) information using multiple tools including Sylph, Groot, and DeepARG, with results normalized through argNorm and aggregated via ToolDistillator.

Key changes:

Introduces a comprehensive metagenomic analysis workflow combining taxonomic assignment (Sylph/Sylph-tax) and AMR detection (Groot/DeepARG)
Implements results uniformization through argNorm for standardized AMR gene reporting
Includes ToolDistillator integration for aggregating and summarizing multi-tool outputs

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
metagenomic-raw-reads-amr-analysis.ga	Main workflow file implementing the analysis pipeline with 24 steps, including quality control, taxonomic profiling, AMR detection, and results aggregation
metagenomic-raw-reads-amr-analysis-tests.yml	Test configuration with Zenodo-hosted test data and output assertions for validating workflow functionality
README.md	Documentation explaining workflow purpose, processing steps, and input requirements
CHANGELOG.md	Version history documenting the initial 1.0 release
.dockstore.yml	Dockstore configuration with workflow metadata, author information including ORCID for one author

workflows/microbiome/metagenomic-raw-reads-amr-analysis/README.md

workflows/microbiome/metagenomic-raw-reads-amr-analysis/.dockstore.yml

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga

...s/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis-tests.yml

workflows/microbiome/metagenomic-raw-reads-amr-analysis/README.md

github-actions · 2025-12-15T10:50:26Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Workflow invocation details

Invocation Messages

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "362d63b6d9a211f0a3dd7c1e527f9306"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp54s6fkpf/files/e/6/0/dataset_e603bb25-1389-47f1-97a5-15286d7e6c44.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp54s6fkpf/files/2/3/1/dataset_231ef066-9708-449f-9e87-1d10f9f8c4ea.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...  [0.002s]
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, 244530.13reads/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 [00:07,  7.21s/chunks]
1chunks [00:07,  7.21s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/145 [00:00<?, ?it/s]
100%|██████████| 145/145 [00:00<00:00, 32835.23it/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__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp54s6fkpf/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 13: 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

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/OceanDNA-c200-v0.3.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp54s6fkpf/files/e/6/0/dataset_e603bb25-1389-47f1-97a5-15286d7e6c44.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp54s6fkpf/files/2/3/1/dataset_231ef066-9708-449f-9e87-1d10f9f8c4ea.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/tmp54s6fkpf/job_working_directory/000/6/outputs/dataset_0f052fb4-393f-45ad-80f5-429b4501892e.dat'  && cp '/tmp/tmp54s6fkpf/job_working_directory/000/6/configs/tmp914hj6gz' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp54s6fkpf/job_working_directory/000/6/outputs/dataset_0f052fb4-393f-45ad-80f5-429b4501892e.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:

2025-12-15T10:39:09.546Z INFO  [sylph::sketch] Sketching paired sequences...
2025-12-15T10:39:09.899Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-12-15T10:39:09.899Z INFO  [sylph::sketch] Finished.
2025-12-15T10:39:09.902Z INFO  [sylph::contain] Obtaining sketches...
2025-12-15T10:45:48.128Z INFO  [sylph::contain] Finished obtaining genome sketches.
2025-12-15T10:45:48.761Z INFO  [sylph::contain] sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp taxonomic profiling; reassigning k-mers for 1 genomes...
2025-12-15T10:45:48.767Z INFO  [sylph::contain] sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp has 1 genomes passing profiling threshold. 
2025-12-15T10:45:48.767Z INFO  [sylph::contain] Finished sample sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp.
2025-12-15T10:45:48.767Z INFO  [sylph::contain] sylph finished.

Standard Output:

Reading metadata: ['OceanDNA'] ...
Processing sylph output file:  /tmp/tmp54s6fkpf/job_working_directory/000/6/outputs/dataset_0f052fb4-393f-45ad-80f5-429b4501892e.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__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp54s6fkpf/files/e/6/0/dataset_e603bb25-1389-47f1-97a5-15286d7e6c44.dat' sanger.gz '/tmp/tmp54s6fkpf/files/2/3/1/dataset_231ef066-9708-449f-9e87-1d10f9f8c4ea.dat' sanger.gz '/tmp/tmp54s6fkpf/job_working_directory/000/7/outputs/dataset_aea444e3-f473-4de3-a650-2910d882457a.dat' '/tmp/tmp54s6fkpf/job_working_directory/000/7/outputs/dataset_359ae2ec-ca2c-4c7f-a14d-e3eedc38adaf.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 127500 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm DeepARG:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp54s6fkpf/files/c/8/9/dataset_c89e105d-4e91-407e-bd90-3e51bf54d5fe.dat' -o '/tmp/tmp54s6fkpf/job_working_directory/000/8/outputs/dataset_926a7f67-a59e-4318-9a26-7d2997ce1853.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp54s6fkpf/job_working_directory/000/8/outputs/dataset_926a7f67-a59e-4318-9a26-7d2997ce1853.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Remove beginning1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

tail -n '+2' '/tmp/tmp54s6fkpf/files/5/a/3/dataset_5a3a341c-13f9-4b4b-82d4-0bd138c6f73a.dat' > '/tmp/tmp54s6fkpf/job_working_directory/000/14/outputs/dataset_586c61a1-81b9-4dcc-a376-0c451f2c179a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
num_lines	`"1"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp54s6fkpf/files/a/e/a/dataset_aea444e3-f473-4de3-a650-2910d882457a.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 '0.95' > '/tmp/tmp54s6fkpf/job_working_directory/000/9/outputs/dataset_3dc38790-faf1-4e78-acec-2c1249f9bd70.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp54s6fkpf/files/a/e/a/dataset_aea444e3-f473-4de3-a650-2910d882457a.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 0.95

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp54s6fkpf/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": "0.95", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp54s6fkpf/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp54s6fkpf/files/9/2/6/dataset_926a7f67-a59e-4318-9a26-7d2997ce1853.dat' '/tmp/tmp54s6fkpf/job_working_directory/000/10/outputs/dataset_d793e6df-e26d-46f3-a77d-3dc9101d9f70.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "362d63b6d9a211f0a3dd7c1e527f9306"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: argNorm Groot:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp54s6fkpf/files/3/d/c/dataset_3dc38790-faf1-4e78-acec-2c1249f9bd70.dat' -o '/tmp/tmp54s6fkpf/job_working_directory/000/11/outputs/dataset_2c812a1b-644d-4cf4-8eda-0ac0f6cbca1c.dat'

Exit Code:

```
1
```

Standard Error:

Traceback (most recent call last):
  File "/usr/local/bin/argnorm", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/usr/local/lib/python3.13/site-packages/argnorm/cli.py", line 61, in main
    result = normalize(args.input,
            tool=args.tool,
            database=args.db,
            skip_on_unsupported_tool=args.hamronization_skip_unsupported_tool
        )
  File "/usr/local/lib/python3.13/site-packages/argnorm/normalize.py", line 35, in normalize
    return norm.run(ifile)
           ~~~~~~~~^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/argnorm/normalizers.py", line 34, in run
    original_annot = self.load_input(input_file)
  File "/usr/local/lib/python3.13/site-packages/argnorm/normalizers.py", line 209, in load_input
    return pd.read_csv(input_file, sep='\t', header=None)
           ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/usr/local/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 620, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/usr/local/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
    return mapping[engine](f, **self.options)
           ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.13/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
    self._reader = parsers.TextReader(src, **kwds)
                   ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "362d63b6d9a211f0a3dd7c1e527f9306"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp54s6fkpf/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp54s6fkpf/files/4/e/0/dataset_4e0c475c-af19-42e0-b12f-e14579ac276d.dat' '/tmp/tmp54s6fkpf/job_working_directory/000/13/outputs/dataset_06a88028-0393-485e-8644-ff1d206edb7f.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator groot --hid '33' '/tmp/tmp54s6fkpf/files/3/d/c/dataset_3dc38790-faf1-4e78-acec-2c1249f9bd70.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 '24' '/tmp/tmp54s6fkpf/files/0/f/0/dataset_0f052fb4-393f-45ad-80f5-429b4501892e.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 '25' '/tmp/tmp54s6fkpf/files/8/b/3/dataset_8b3ae409-5838-43f3-a46e-cb3bdaf6919e.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 '41' '/tmp/tmp54s6fkpf/files/0/6/a/dataset_06a88028-0393-485e-8644-ff1d206edb7f.dat' --analysis_software_version '' --reference_database_version '' -o 'tooldistillator_folder/argnorm_3_output.json' | tee 'XXXX' &&  tooldistillator tabular_file --hid '45' '/tmp/tmp54s6fkpf/files/5/8/6/dataset_586c61a1-81b9-4dcc-a376-0c451f2c179a.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 '15' '/tmp/tmp54s6fkpf/files/c/8/9/dataset_c89e105d-4e91-407e-bd90-3e51bf54d5fe.dat' --analysis_software_version '1.0.4+galaxy1' --reference_database_version 'deeparg_1.0.4-07112025' --report_ARG_merged_path '/tmp/tmp54s6fkpf/files/0/2/d/dataset_02d0f839-3f98-4d73-a058-8b089dc78d5e.dat' --report_ARG_merged_hid '16' --report_ARG_merged_quant_subtype_path '/tmp/tmp54s6fkpf/files/0/c/0/dataset_0c0bc2b6-bfe7-463d-8739-83e9678eba6e.dat' --report_ARG_merged_quant_subtype_hid '17' --report_ARG_merged_quant_type_path '/tmp/tmp54s6fkpf/files/1/c/5/dataset_1c51928a-d688-4cca-a6b0-f48ed2108921.dat' --report_ARG_merged_quant_type_hid '18' -o 'tooldistillator_folder/deeparg_5_output.json' | tee 'XXXX' &&  tooldistillator argnorm --hid '35' '/tmp/tmp54s6fkpf/files/d/7/9/dataset_d793e6df-e26d-46f3-a77d-3dc9101d9f70.dat' --analysis_software_version '1.0.0' --reference_database_version '' -o 'tooldistillator_folder/argnorm_6_output.json' | tee 'XXXX'

Exit Code:

```
0
```

Standard Error:

+ mkdir tooldistillator_folder
+ tooldistillator groot --hid 33 /tmp/tmp54s6fkpf/files/3/d/c/dataset_3dc38790-faf1-4e78-acec-2c1249f9bd70.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
12/15/2025 10:48:42 AM: interfaces.py: Input file is empty
+ tooldistillator sylph --hid 24 /tmp/tmp54s6fkpf/files/0/f/0/dataset_0f052fb4-393f-45ad-80f5-429b4501892e.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
12/15/2025 10:48:44 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/0/f/0/dataset_0f052fb4-393f-45ad-80f5-429b4501892e.dat
12/15/2025 10:48:44 AM: sylphio.py: add Sylph report file
+ tooldistillator sylphtax --hid 25 /tmp/tmp54s6fkpf/files/8/b/3/dataset_8b3ae409-5838-43f3-a46e-cb3bdaf6919e.dat --analysis_software_version 0.8.1+galaxy0 --reference_database_version sylph_tax_downloaded_08112025 -o tooldistillator_folder/sylphtax_2_output.json
+ tee XXXX
12/15/2025 10:48:45 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/8/b/3/dataset_8b3ae409-5838-43f3-a46e-cb3bdaf6919e.dat
12/15/2025 10:48:45 AM: sylphtaxio.py: add Sylph-tax merge report file
+ tooldistillator argnorm --hid 41 /tmp/tmp54s6fkpf/files/0/6/a/dataset_06a88028-0393-485e-8644-ff1d206edb7f.dat --analysis_software_version '' --reference_database_version '' -o tooldistillator_folder/argnorm_3_output.json
+ tee XXXX
12/15/2025 10:48:47 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/0/6/a/dataset_06a88028-0393-485e-8644-ff1d206edb7f.dat
12/15/2025 10:48:47 AM: argnormio.py: add argNorm report file
+ tooldistillator tabular_file --hid 45 /tmp/tmp54s6fkpf/files/5/8/6/dataset_586c61a1-81b9-4dcc-a376-0c451f2c179a.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
12/15/2025 10:48:49 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/5/8/6/dataset_586c61a1-81b9-4dcc-a376-0c451f2c179a.dat
+ tooldistillator deeparg --hid 15 /tmp/tmp54s6fkpf/files/c/8/9/dataset_c89e105d-4e91-407e-bd90-3e51bf54d5fe.dat --analysis_software_version 1.0.4+galaxy1 --reference_database_version deeparg_1.0.4-07112025 --report_ARG_merged_path /tmp/tmp54s6fkpf/files/0/2/d/dataset_02d0f839-3f98-4d73-a058-8b089dc78d5e.dat --report_ARG_merged_hid 16 --report_ARG_merged_quant_subtype_path /tmp/tmp54s6fkpf/files/0/c/0/dataset_0c0bc2b6-bfe7-463d-8739-83e9678eba6e.dat --report_ARG_merged_quant_subtype_hid 17 --report_ARG_merged_quant_type_path /tmp/tmp54s6fkpf/files/1/c/5/dataset_1c51928a-d688-4cca-a6b0-f48ed2108921.dat --report_ARG_merged_quant_type_hid 18 -o tooldistillator_folder/deeparg_5_output.json
+ tee XXXX
12/15/2025 10:48:50 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/c/8/9/dataset_c89e105d-4e91-407e-bd90-3e51bf54d5fe.dat
12/15/2025 10:48:50 AM: deepargio.py: add DeepARG report file
12/15/2025 10:48:50 AM: deepargio.py: add DeepARG ARG merged report file
12/15/2025 10:48:50 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/0/2/d/dataset_02d0f839-3f98-4d73-a058-8b089dc78d5e.dat
12/15/2025 10:48:50 AM: deepargio.py: add DeepARG ARG merged quant subtype report file
12/15/2025 10:48:50 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/0/c/0/dataset_0c0bc2b6-bfe7-463d-8739-83e9678eba6e.dat
12/15/2025 10:48:50 AM: deepargio.py: add DeepARG ARG merged quant type report file
12/15/2025 10:48:50 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/1/c/5/dataset_1c51928a-d688-4cca-a6b0-f48ed2108921.dat
+ tooldistillator argnorm --hid 35 /tmp/tmp54s6fkpf/files/d/7/9/dataset_d793e6df-e26d-46f3-a77d-3dc9101d9f70.dat --analysis_software_version 1.0.0 --reference_database_version '' -o tooldistillator_folder/argnorm_6_output.json
+ tee XXXX
12/15/2025 10:48:52 AM: interfaces.py: Treatment of /tmp/tmp54s6fkpf/files/d/7/9/dataset_d793e6df-e26d-46f3-a77d-3dc9101d9f70.dat
12/15/2025 10:48:52 AM: argnormio.py: add argNorm report file

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/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": 18, "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": 13, "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": 14, "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": 22, "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": 26, "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": 6, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "deeparg_1.0.4-07112025", "report_arg_merged_path": {"values": [{"id": 7, "src": "dce"}]}, "report_arg_merged_quant_subtype_path": {"values": [{"id": 8, "src": "dce"}]}, "report_arg_merged_quant_type_path": {"values": [{"id": 9, "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": 19, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "tool_list": "argnorm"}}]}

Step 24: 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

Command Line:

tooldistillator --version && mkdir -p input_files && cp '/tmp/tmp54s6fkpf/files/1/f/4/dataset_1f49385d-942b-4ace-8671-b326c504c3d7.dat' ./input_files/ && cp '/tmp/tmp54s6fkpf/files/d/5/d/dataset_d5d5d9f4-d67f-4df4-9ee5-f71bad6347db.dat' ./input_files/ && cp '/tmp/tmp54s6fkpf/files/0/0/a/dataset_00aff9d6-853f-46bc-ae46-ddb88ceff707.dat' ./input_files/ && cp '/tmp/tmp54s6fkpf/files/4/3/4/dataset_4341d0e5-5dc4-4f72-9ffb-89663ea6e2bf.dat' ./input_files/ && cp '/tmp/tmp54s6fkpf/files/a/6/c/dataset_a6cc4de6-5612-45f0-8fb5-d1853b6edf23.dat' ./input_files/ && cp '/tmp/tmp54s6fkpf/files/c/f/9/dataset_cf92cf97-31fd-406c-82cc-3fdcdf0fccfc.dat' ./input_files/ && cp '/tmp/tmp54s6fkpf/files/d/0/8/dataset_d084092c-3640-4c5a-a930-ca81bd5dc7bf.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__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg : Minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Sylph database:
- step_state: scheduled
Step 7: Sylph tax database:
- step_state: scheduled
Step 8: Groot : Average base pair length of reads of your sample:
- step_state: scheduled
Step 9: Groot : Minimum coverage for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp54s6fkpf/job_working_directory/000/3/outputs/dataset_4e0c475c-af19-42e0-b12f-e14579ac276d.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp54s6fkpf/job_working_directory/000/3/outputs/dataset_4e0c475c-af19-42e0-b12f-e14579ac276d.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"362d63b6d9a211f0a3dd7c1e527f9306"`
chromInfo	`"/tmp/tmp54s6fkpf/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"}}]`

Other invocation details
- history_id
  - 05dc1b6053601e92
- history_state
  - error
- invocation_id
  - 05dc1b6053601e92
- invocation_state
  - scheduled
- workflow_id
  - 05dc1b6053601e92

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga

Co-authored-by: Bérénice Batut <berenice.batut@gmail.com>

github-actions · 2025-12-15T13:58:59Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 (version 9.5+galaxy2)","err_code":0}

github-actions · 2025-12-15T14:25:50Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

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

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2 (version 9.5+galaxy2)","err_code":0}

…tagenomics raw reads is in development

… from metagenomics raw reads is in development" This reverts commit 77f5ecc.

bebatut

Thanks a lot @hugolefeuvre!
I made suggestions (mostly to rename inputs/outputs and hide intermediate outputs).
As we already discussed, it would be really useful to have a MultiQC report at the end to have one report aggregating all results.

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga

bebatut · 2025-12-18T12:50:54Z

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga

+        "paired-collection(s)",
+        "fastq",
+        "ABRomics",
+        "raw-reads"


Suggested change

"raw-reads"

"short-reads"

bebatut · 2025-12-18T12:50:59Z

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga

+        }
+    },
+    "tags": [
+        "Metagenomics",


Suggested change

"Metagenomics",

"metagenomics",

bebatut · 2025-12-18T12:51:18Z

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga

+    "tags": [
+        "Metagenomics",
+        "paired-collection(s)",
+        "fastq",


Suggested change

"fastq",

"taxonomy",

"Antibiotic Resistance Genes",

workflows/microbiome/metagenomic-raw-reads-amr-analysis/README.md

bebatut

Thanks a lot @hugolefeuvre!
I made suggestions (mostly to rename inputs/outputs and hide intermediate outputs).
As we already discussed, it would be really useful to have a MultiQC report at the end to have one report aggregating all results.

Co-authored-by: Bérénice Batut <berenice.batut@gmail.com>

github-actions · 2025-12-19T09:02:16Z

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: ARG Database for DeepARG:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "8a8db2e4dcb811f09c9700224805ce8d"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: 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

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmpy0577ltx/files/c/d/d/dataset_cddc2cbe-9fbf-4fb9-8d4e-8818d47c42d9.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmpy0577ltx/files/2/1/d/dataset_21d3bb85-7e41-4683-8945-b8c3daff42e0.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...  [0.002s]
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, 261412.62reads/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 [00:07,  7.51s/chunks]
1chunks [00:07,  7.51s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/145 [00:00<?, ?it/s]
100%|██████████| 145/145 [00:00<00:00, 41859.32it/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__	`"8a8db2e4dcb811f09c9700224805ce8d"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpy0577ltx/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 13: 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

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/OceanDNA-c200-v0.3.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmpy0577ltx/files/c/d/d/dataset_cddc2cbe-9fbf-4fb9-8d4e-8818d47c42d9.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmpy0577ltx/files/2/1/d/dataset_21d3bb85-7e41-4683-8945-b8c3daff42e0.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/tmpy0577ltx/job_working_directory/000/6/outputs/dataset_51050cd7-faf3-4e46-a5fd-908380d52321.dat'  && cp '/tmp/tmpy0577ltx/job_working_directory/000/6/configs/tmpxba4q9q_' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmpy0577ltx/job_working_directory/000/6/outputs/dataset_51050cd7-faf3-4e46-a5fd-908380d52321.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:

2025-12-19T08:57:16.379Z INFO  [sylph::sketch] Sketching paired sequences...
2025-12-19T08:57:16.624Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-12-19T08:57:16.624Z INFO  [sylph::sketch] Finished.
2025-12-19T08:57:16.627Z INFO  [sylph::contain] Obtaining sketches...
2025-12-19T08:57:41.517Z INFO  [sylph::contain] Finished obtaining genome sketches.
2025-12-19T08:57:42.312Z INFO  [sylph::contain] sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp taxonomic profiling; reassigning k-mers for 1 genomes...
2025-12-19T08:57:42.321Z INFO  [sylph::contain] sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp has 1 genomes passing profiling threshold. 
2025-12-19T08:57:42.321Z INFO  [sylph::contain] Finished sample sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp.
2025-12-19T08:57:42.321Z INFO  [sylph::contain] sylph finished.

Standard Output:

Reading metadata: ['OceanDNA'] ...
Processing sylph output file:  /tmp/tmpy0577ltx/job_working_directory/000/6/outputs/dataset_51050cd7-faf3-4e46-a5fd-908380d52321.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__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/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: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpy0577ltx/files/c/d/d/dataset_cddc2cbe-9fbf-4fb9-8d4e-8818d47c42d9.dat' sanger.gz '/tmp/tmpy0577ltx/files/2/1/d/dataset_21d3bb85-7e41-4683-8945-b8c3daff42e0.dat' sanger.gz '/tmp/tmpy0577ltx/job_working_directory/000/7/outputs/dataset_40313a8d-a11d-4d5a-b56c-b3cd361fa143.dat' '/tmp/tmpy0577ltx/job_working_directory/000/7/outputs/dataset_7445ae30-8385-4d8c-870a-3454bdd66073.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 127500 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm on DeepARG ouput:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmpy0577ltx/files/7/8/a/dataset_78ace45f-0046-4d29-b7b5-1c9b9f42027f.dat' -o '/tmp/tmpy0577ltx/job_working_directory/000/8/outputs/dataset_ffe012f2-2fad-45aa-ab0a-1e9a9446d8ea.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpy0577ltx/job_working_directory/000/8/outputs/dataset_ffe012f2-2fad-45aa-ab0a-1e9a9446d8ea.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Remove beginning1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

tail -n '+2' '/tmp/tmpy0577ltx/files/0/1/3/dataset_013ca906-cc9c-4edb-8dd6-e3263db9a5a0.dat' > '/tmp/tmpy0577ltx/job_working_directory/000/12/outputs/dataset_384a3e3f-a6de-432a-8ab5-8433b3770030.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
num_lines	`"1"`

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmpy0577ltx/files/4/0/3/dataset_40313a8d-a11d-4d5a-b56c-b3cd361fa143.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/tmpy0577ltx/job_working_directory/000/9/outputs/dataset_da9b984a-87cb-48b6-8041-716581befaf9.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmpy0577ltx/files/4/0/3/dataset_40313a8d-a11d-4d5a-b56c-b3cd361fa143.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__	`"8a8db2e4dcb811f09c9700224805ce8d"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpy0577ltx/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 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpy0577ltx/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpy0577ltx/files/f/f/e/dataset_ffe012f2-2fad-45aa-ab0a-1e9a9446d8ea.dat' '/tmp/tmpy0577ltx/job_working_directory/000/10/outputs/dataset_1a0bcfdb-563a-4c46-8d29-1958ea811bb4.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "8a8db2e4dcb811f09c9700224805ce8d"
      
      input {"values": [{"id": 19, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: argNorm on Groot output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmpy0577ltx/files/d/a/9/dataset_da9b984a-87cb-48b6-8041-716581befaf9.dat' -o '/tmp/tmpy0577ltx/job_working_directory/000/11/outputs/dataset_d2fc2938-7c2f-4b7b-82ca-02df2df99f73.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpy0577ltx/job_working_directory/000/11/outputs/dataset_d2fc2938-7c2f-4b7b-82ca-02df2df99f73.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: ARG Database for Groot:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "8a8db2e4dcb811f09c9700224805ce8d"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpy0577ltx/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpy0577ltx/files/d/2/f/dataset_d2fc2938-7c2f-4b7b-82ca-02df2df99f73.dat' '/tmp/tmpy0577ltx/job_working_directory/000/15/outputs/dataset_ad6b21a4-740d-4783-a034-3758f2cc7481.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator groot --hid '33' '/tmp/tmpy0577ltx/files/d/a/9/dataset_da9b984a-87cb-48b6-8041-716581befaf9.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 '24' '/tmp/tmpy0577ltx/files/5/1/0/dataset_51050cd7-faf3-4e46-a5fd-908380d52321.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 '25' '/tmp/tmpy0577ltx/files/6/c/e/dataset_6ce35750-7f6a-4fad-b481-d4e894f9e3cc.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/tmpy0577ltx/files/a/d/6/dataset_ad6b21a4-740d-4783-a034-3758f2cc7481.dat' --analysis_software_version '' --reference_database_version '' -o 'tooldistillator_folder/argnorm_3_output.json' | tee 'XXXX' &&  tooldistillator tabular_file --hid '41' '/tmp/tmpy0577ltx/files/3/8/4/dataset_384a3e3f-a6de-432a-8ab5-8433b3770030.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 '15' '/tmp/tmpy0577ltx/files/7/8/a/dataset_78ace45f-0046-4d29-b7b5-1c9b9f42027f.dat' --analysis_software_version '1.0.4+galaxy1' --reference_database_version 'deeparg_1.0.4-07112025' --report_ARG_merged_path '/tmp/tmpy0577ltx/files/9/4/4/dataset_94469b7a-c32b-4652-a6c3-177306eaddcd.dat' --report_ARG_merged_hid '16' --report_ARG_merged_quant_subtype_path '/tmp/tmpy0577ltx/files/5/f/a/dataset_5fae4bcd-d46f-41e8-91e7-8ad511d97a7e.dat' --report_ARG_merged_quant_subtype_hid '17' --report_ARG_merged_quant_type_path '/tmp/tmpy0577ltx/files/8/7/8/dataset_8788ec7c-d2db-4d32-bd22-812634ec1e80.dat' --report_ARG_merged_quant_type_hid '18' -o 'tooldistillator_folder/deeparg_5_output.json' | tee 'XXXX' &&  tooldistillator argnorm --hid '35' '/tmp/tmpy0577ltx/files/1/a/0/dataset_1a0bcfdb-563a-4c46-8d29-1958ea811bb4.dat' --analysis_software_version '1.0.0' --reference_database_version '' -o 'tooldistillator_folder/argnorm_6_output.json' | tee 'XXXX'

Exit Code:

```
0
```

Standard Error:

+ mkdir tooldistillator_folder
+ tooldistillator groot --hid 33 /tmp/tmpy0577ltx/files/d/a/9/dataset_da9b984a-87cb-48b6-8041-716581befaf9.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
12/19/2025 09:00:16 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/d/a/9/dataset_da9b984a-87cb-48b6-8041-716581befaf9.dat
12/19/2025 09:00:16 AM: grootio.py: add Groot report file
+ tooldistillator sylph --hid 24 /tmp/tmpy0577ltx/files/5/1/0/dataset_51050cd7-faf3-4e46-a5fd-908380d52321.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
12/19/2025 09:00:18 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/5/1/0/dataset_51050cd7-faf3-4e46-a5fd-908380d52321.dat
12/19/2025 09:00:18 AM: sylphio.py: add Sylph report file
+ tooldistillator sylphtax --hid 25 /tmp/tmpy0577ltx/files/6/c/e/dataset_6ce35750-7f6a-4fad-b481-d4e894f9e3cc.dat --analysis_software_version 0.8.1+galaxy0 --reference_database_version sylph_tax_downloaded_08112025 -o tooldistillator_folder/sylphtax_2_output.json
+ tee XXXX
12/19/2025 09:00:20 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/6/c/e/dataset_6ce35750-7f6a-4fad-b481-d4e894f9e3cc.dat
12/19/2025 09:00:20 AM: sylphtaxio.py: add Sylph-tax merge report file
+ tooldistillator argnorm --hid 46 /tmp/tmpy0577ltx/files/a/d/6/dataset_ad6b21a4-740d-4783-a034-3758f2cc7481.dat --analysis_software_version '' --reference_database_version '' -o tooldistillator_folder/argnorm_3_output.json
+ tee XXXX
12/19/2025 09:00:22 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/a/d/6/dataset_ad6b21a4-740d-4783-a034-3758f2cc7481.dat
12/19/2025 09:00:22 AM: argnormio.py: add argNorm report file
+ tooldistillator tabular_file --hid 41 /tmp/tmpy0577ltx/files/3/8/4/dataset_384a3e3f-a6de-432a-8ab5-8433b3770030.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
12/19/2025 09:00:23 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/3/8/4/dataset_384a3e3f-a6de-432a-8ab5-8433b3770030.dat
+ tooldistillator deeparg --hid 15 /tmp/tmpy0577ltx/files/7/8/a/dataset_78ace45f-0046-4d29-b7b5-1c9b9f42027f.dat --analysis_software_version 1.0.4+galaxy1 --reference_database_version deeparg_1.0.4-07112025 --report_ARG_merged_path /tmp/tmpy0577ltx/files/9/4/4/dataset_94469b7a-c32b-4652-a6c3-177306eaddcd.dat --report_ARG_merged_hid 16 --report_ARG_merged_quant_subtype_path /tmp/tmpy0577ltx/files/5/f/a/dataset_5fae4bcd-d46f-41e8-91e7-8ad511d97a7e.dat --report_ARG_merged_quant_subtype_hid 17 --report_ARG_merged_quant_type_path /tmp/tmpy0577ltx/files/8/7/8/dataset_8788ec7c-d2db-4d32-bd22-812634ec1e80.dat --report_ARG_merged_quant_type_hid 18 -o tooldistillator_folder/deeparg_5_output.json
+ tee XXXX
12/19/2025 09:00:25 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/7/8/a/dataset_78ace45f-0046-4d29-b7b5-1c9b9f42027f.dat
12/19/2025 09:00:25 AM: deepargio.py: add DeepARG report file
12/19/2025 09:00:25 AM: deepargio.py: add DeepARG ARG merged report file
12/19/2025 09:00:25 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/9/4/4/dataset_94469b7a-c32b-4652-a6c3-177306eaddcd.dat
12/19/2025 09:00:25 AM: deepargio.py: add DeepARG ARG merged quant subtype report file
12/19/2025 09:00:25 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/5/f/a/dataset_5fae4bcd-d46f-41e8-91e7-8ad511d97a7e.dat
12/19/2025 09:00:25 AM: deepargio.py: add DeepARG ARG merged quant type report file
12/19/2025 09:00:25 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/8/7/8/dataset_8788ec7c-d2db-4d32-bd22-812634ec1e80.dat
+ tooldistillator argnorm --hid 35 /tmp/tmpy0577ltx/files/1/a/0/dataset_1a0bcfdb-563a-4c46-8d29-1958ea811bb4.dat --analysis_software_version 1.0.0 --reference_database_version '' -o tooldistillator_folder/argnorm_6_output.json
+ tee XXXX
12/19/2025 09:00:27 AM: interfaces.py: Treatment of /tmp/tmpy0577ltx/files/1/a/0/dataset_1a0bcfdb-563a-4c46-8d29-1958ea811bb4.dat
12/19/2025 09:00:27 AM: argnormio.py: add argNorm report file

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/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": 18, "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": 13, "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": 14, "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": 26, "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": 24, "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": 6, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": "deeparg_1.0.4-07112025", "report_arg_merged_path": {"values": [{"id": 7, "src": "dce"}]}, "report_arg_merged_quant_subtype_path": {"values": [{"id": 8, "src": "dce"}]}, "report_arg_merged_quant_type_path": {"values": [{"id": 9, "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": 19, "src": "dce"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "tool_list": "argnorm"}}]}

Step 24: 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

Command Line:

tooldistillator --version && mkdir -p input_files && cp '/tmp/tmpy0577ltx/files/a/6/0/dataset_a60e6cca-5c43-4000-862a-f196ccdbbbb4.dat' ./input_files/ && cp '/tmp/tmpy0577ltx/files/5/3/f/dataset_53f13029-6dda-4333-a609-166a802234d6.dat' ./input_files/ && cp '/tmp/tmpy0577ltx/files/f/1/2/dataset_f12c9a71-2cf4-4bcc-9087-0d9271c68136.dat' ./input_files/ && cp '/tmp/tmpy0577ltx/files/d/a/b/dataset_dabcd4e3-cd2d-4266-a09e-06ad294d179d.dat' ./input_files/ && cp '/tmp/tmpy0577ltx/files/c/e/9/dataset_ce974ae6-84bf-4e57-8979-cc5a1a75a1cc.dat' ./input_files/ && cp '/tmp/tmpy0577ltx/files/b/e/6/dataset_be6e672f-aba3-46d6-b4e4-d00fd743c307.dat' ./input_files/ && cp '/tmp/tmpy0577ltx/files/e/e/6/dataset_ee69cfaa-885b-409f-8339-ef239312be1e.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__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: ARG Database used by Groot for ARGnorm:
- step_state: scheduled
Step 5: Minimum probability for considering a reads as ARG-like in deepARG:
- step_state: scheduled
Step 6: Taxonomy Profiling Database for Sylph:
- step_state: scheduled
Step 7: Taxonomic Information Database for Sylph:
- step_state: scheduled
Step 8: Average Read Length for Groot:
- step_state: scheduled
Step 9: Coverage Threshold for Groot to Report an ARG:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpy0577ltx/job_working_directory/000/3/outputs/dataset_ba26d2df-a0b5-4d63-8c55-6b785c098cec.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpy0577ltx/job_working_directory/000/3/outputs/dataset_ba26d2df-a0b5-4d63-8c55-6b785c098cec.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8a8db2e4dcb811f09c9700224805ce8d"`
chromInfo	`"/tmp/tmpy0577ltx/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"}}]`

Other invocation details
- history_id
  - 1fd899d285c6d1f5
- history_state
  - ok
- invocation_id
  - 1fd899d285c6d1f5
- invocation_state
  - scheduled
- workflow_id
  - 1fd899d285c6d1f5

hugolefeuvre · 2025-12-19T09:54:04Z

As we already discussed, it would be really useful to have a MultiQC report at the end to have one report aggregating all results.

I made the rest of the suggested changes.
For multiQC, deepARG and sylph's output does not work :
yaml.scanner.ScannerError: while scanning for the next token found character '\t' that cannot start any token in "<unicode string>", line 1, column 4: ARG query-start query-end read_id p ...
Same for Sylph

hugolefeuvre and others added 4 commits October 14, 2025 18:14

init raw reads analysis metag data wf

3b5bd25

workflow modifications

556057d

update tooldistillator version to 1.0.3

d41a0fd

Merge branch 'galaxyproject:main' into raw_reads_metaG

c0a60e6

add cvmfs DBs identifier

1dc8266

add argnorm groot DB input and update tooldistillator

85fc598

rename wf with amr information

d1cf861

delete old repo name

56d60d1

hugolefeuvre added 4 commits November 20, 2025 11:16

modify output name and label, remove select from input

06a562e

miss version

1fd2998

modify inout name in test file

9919690

modify deeparg input in test file

daf6bbc

hugolefeuvre requested a review from Copilot December 11, 2025 15:06

Copilot started reviewing on behalf of hugolefeuvre December 11, 2025 15:07 View session

Copilot AI reviewed Dec 11, 2025

View reviewed changes

hugolefeuvre added 2 commits December 15, 2025 11:26

change sylph db + change test input + update with copilot review

f4b5aaa

update input in test.yml file

ac9d31b

modify input parameter name

f1317a0

bebatut reviewed Dec 15, 2025

View reviewed changes

workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga Outdated Show resolved Hide resolved

Update workflow name

dcc17f4

Co-authored-by: Bérénice Batut <berenice.batut@gmail.com>

hugolefeuvre added 2 commits December 15, 2025 16:00

remove taxonomic part because an other WF related to taxonomy from me…

77f5ecc

…tagenomics raw reads is in development

Revert "remove taxonomic part because an other WF related to taxonomy…

eed077e

… from metagenomics raw reads is in development" This reverts commit 77f5ecc.

bebatut reviewed Dec 18, 2025

View reviewed changes

hugolefeuvre and others added 4 commits December 18, 2025 14:30

Apply suggestions from code review

086f8bb

Co-authored-by: Bérénice Batut <berenice.batut@gmail.com>

lint modification and adapt input in test.yml

57a75cc

minor changes for review

874b17f

add version in .ga

29d8414

Metagenomic raw reads analysis workflow without assembly #1014

Are you sure you want to change the base?

Metagenomic raw reads analysis workflow without assembly #1014

Uh oh!

Conversation

hugolefeuvre commented Nov 3, 2025

Uh oh!

hugolefeuvre commented Nov 3, 2025

Uh oh!

github-actions bot commented Nov 3, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

github-actions bot commented Nov 11, 2025

Test Results (powered by Planemo)

Test Summary

Uh oh!

github-actions bot commented Nov 12, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

hugolefeuvre commented Nov 12, 2025

Uh oh!

github-actions bot commented Nov 14, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Workflow invocation details

Uh oh!

github-actions bot commented Nov 14, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

github-actions bot commented Nov 20, 2025

Test Results (powered by Planemo)

Test Summary

Uh oh!

github-actions bot commented Nov 20, 2025

Test Results (powered by Planemo)

Test Summary

Uh oh!

github-actions bot commented Nov 20, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

github-actions bot commented Nov 20, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

hugolefeuvre commented Dec 9, 2025

Uh oh!

mvdbeek commented Dec 9, 2025

Uh oh!

hugolefeuvre commented Dec 9, 2025

Uh oh!

mvdbeek commented Dec 9, 2025

Uh oh!

hugolefeuvre commented Dec 10, 2025

Uh oh!

mvdbeek commented Dec 10, 2025

Uh oh!

hugolefeuvre commented Dec 10, 2025

Uh oh!

mvdbeek commented Dec 10, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

hugolefeuvre commented Dec 10, 2025

Uh oh!

hugolefeuvre commented Dec 10, 2025

Uh oh!

bebatut commented Dec 11, 2025

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

mvdbeek commented Dec 10, 2025 •

edited

Loading