add "VirDetectorGalaxy" workflow for virial analysis from nanopore data. by Smkingsize · Pull Request #1102 · galaxyproject/iwc

Smkingsize · 2026-02-11T09:06:09Z

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.

This workflow is the work of my bachelor thesis based on the pipeline published in the paper:
https://academic.oup.com/bioinformatics/article/41/2/btaf029/7965895?login=false#506671144

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

github-actions · 2026-02-11T09:19:18Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ VirDetectorGalaxy.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"1":{"db_opts|database":"Parameter 'database': invalid options ('nt_2024-08-15') were selected (valid options: /cvmfs/data.galaxyproject.org/byhand/blastdb/phiX/phiX,13apr2014-htgs,17apr2014-nt,nt_2023-09-01,refseq_mitochondrion,20apr2014-wgs) Using default: 'None'."}}}

…ceeded this indicates other tools ran also correctly!

github-actions · 2026-02-11T12:54:12Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ VirDetectorGalaxy.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"1":{"db_opts|database":"Parameter 'database': invalid options ('nt_2024-08-15') were selected (valid options: refseq_mitochondrion,20apr2014-wgs,/cvmfs/data.galaxyproject.org/byhand/blastdb/phiX/phiX,17apr2014-nt,nt_2023-09-01,13apr2014-htgs) Using default: 'None'."}}}

github-actions · 2026-02-11T13:24:00Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ VirDetectorGalaxy.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"1":{"db_opts|database":"Parameter 'database': invalid options ('nt_2024-08-15') were selected (valid options: 20apr2014-wgs,/cvmfs/data.galaxyproject.org/byhand/blastdb/phiX/phiX,nt_2023-09-01,13apr2014-htgs,17apr2014-nt,refseq_mitochondrion) Using default: 'None'."}}}

Smkingsize · 2026-02-11T13:49:58Z

for some reason the database I am using for Blast nt_2024-08-15 is thought to be invalid option :/

Solution: make databases configurable by the users

mvdbeek · 2026-02-11T17:00:35Z

Yes, I was going to suggest that. We don't have the same database options available across all users so making this configurable is the right call. You can add a text parameter and connect it to the database selection.

…t are available on al servers for testing!

github-actions · 2026-02-11T21:34:40Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ VirDetectorGalaxy.ga_0

Execution Problem:

File [/home/runner/work/iwc/iwc/workflows/virology/generic-nanopore-virial-analysis/test-data/Fastq Input Collection_ERR1248114.fastqsanger.gz] does not exist - parent directory [/home/runner/work/iwc/iwc/workflows/virology/generic-nanopore-virial-analysis/test-data] does not exist, cwd is [/home/runner/work/iwc/iwc]

github-actions · 2026-02-12T11:29:01Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ VirDetectorGalaxy.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Fastq Input Collection:
- step_state: scheduled
Step 2: Host/Contaminant Reference Genome:
- step_state: scheduled
Step 3: Profile of preset options for the mapping (long-read):
- step_state: scheduled
Step 4: References:
- step_state: scheduled
Step 5: Perform Metagenomic Analysis:
- step_state: scheduled
Step 6: KMA Index:
- step_state: scheduled
Step 7: Kraken2 Database:
- step_state: scheduled
Step 8: Blast Database:
- step_state: scheduled
Step 9: Maximum likelihood phylogeny:
- step_state: scheduled
Step 10: Bayesian phylogeny:
- step_state: scheduled

Step 11: Trimming (Chopper) 2 (toolshed.g2.bx.psu.edu/repos/iuc/chopper/chopper/0.12.0+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/chopper:0.12.0--hcdda2d0_0

Command Line:

chopper  --input /tmp/tmpfplbed14/files/5/8/c/dataset_58cd873d-22d9-4def-8ae0-f21c01032dfc.dat   --quality 8  --maxqual 60  --minlength 200  --maxlength 20000     --maxgc 1.0    | gzip > /tmp/tmpfplbed14/job_working_directory/000/5/outputs/dataset_5720ef49-9a15-4aec-a665-891f960c3016.dat

Exit Code:

```
0
```

Standard Error:

```
Kept 22364 reads out of 26826 reads
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contam	`None`
dbkey	`"?"`
option_params	`{"headcrop": "0", "maxgc": "1.0", "maxlength": "20000", "maxqual": "60", "mingc": "0.0", "minlength": "200", "quality": "8", "tailcrop": "0", "trim": "0"}`
output_params	`{"inverse": false}`

Step 12: Compare Reads Quality (pre-trimming) (toolshed.g2.bx.psu.edu/repos/iuc/nanocomp/nanocomp/1.25.6+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/nanocomp:1.25.6--pyhdfd78af_0

Command Line:

ln -sf '/tmp/tmpfplbed14/files/5/8/c/dataset_58cd873d-22d9-4def-8ae0-f21c01032dfc.dat' 'ERR1248114.fastqsanger.gz' &&  NanoComp  --make_no_static  --threads ${GALAXY_SLOTS:-4}  --fastq  'ERR1248114.fastqsanger.gz'   --plot violin      --verbose >& /tmp/tmpfplbed14/job_working_directory/000/6/outputs/dataset_d1c6d7cc-e72c-4e1a-ab03-212eb8865590.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filters	`{"maxlength": null, "minlength": null}`
inputs	`{"input_type": {"__current_case__": 0, "input_data": {"values": [{"id": 1, "src": "hdca"}]}, "input_type_selector": "fastq"}}`
output_options	`{"tsv_stats": false}`
plot_options	`{"colors": null, "names": null, "plot": "violin", "title": null}`

Step 13: Map to boolean (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 ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": null, "mappings": [], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 0, "on_unmapped": "input"}`

Step 14: Ref Assembly? (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 ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 4, "input_param": null, "mappings": [], "type": "data"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 0, "on_unmapped": "input"}`

Step 15: Compare Reads Quality (post-trimming) (toolshed.g2.bx.psu.edu/repos/iuc/nanocomp/nanocomp/1.25.6+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/nanocomp:1.25.6--pyhdfd78af_0

Command Line:

ln -sf '/tmp/tmpfplbed14/files/5/7/2/dataset_5720ef49-9a15-4aec-a665-891f960c3016.dat' '_ERR1248114.fastqsanger.gz' &&  NanoComp  --make_no_static  --threads ${GALAXY_SLOTS:-4}  --fastq  '_ERR1248114.fastqsanger.gz'   --plot violin      --verbose >& /tmp/tmpfplbed14/job_working_directory/000/9/outputs/dataset_4607db28-7e56-47fa-95a9-628fd5a18e6f.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filters	`{"maxlength": null, "minlength": null}`
inputs	`{"input_type": {"__current_case__": 0, "input_data": {"values": [{"id": 3, "src": "hdca"}]}, "input_type_selector": "fastq"}}`
output_options	`{"tsv_stats": false}`
plot_options	`{"colors": null, "names": null, "plot": "violin", "title": null}`

Step 16: Host Removal:

step_state: scheduled

Subworkflow Steps

Step 1: Host/Contaminant Reference Genome (long-reads):
- step_state: scheduled
Step 2: Long-reads:
- step_state: scheduled
Step 3: Profile of preset options for the mapping (long-read):
- step_state: scheduled

Step 4: minimap2 (toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9507e811f189517c1e52058f08"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": null, "fastq_input1": {"values": [{"id": 5, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 0, "ref_file": null, "reference_source_selector": "cached"}`

Step 5: QualiMap (toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9507e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicate_skipping	`"0"`
per_base_coverage	`false`
plot_specific	`{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": true}`
stats_regions	`{"__current_case__": 0, "region_select": "all"}`

Step 6: Split BAM (toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"fce87a9507e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: Flatten collection (__FLATTEN__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is skipped
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "fce87a9507e811f189517c1e52058f08"
      
      input {"values": [{"id": 5, "src": "hdca"}]}
      
      join_identifier "_"

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.22+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9507e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
copy_arb_tags	`None`
copy_tags	`false`
dbkey	`"?"`
exclusive_filter	`["256", "2048"]`
exclusive_filter_all	`None`
idxout_cond	`{"__current_case__": 0, "idxout_select": "no"}`
inclusive_filter	`None`
output_fmt_cond	`{"__current_case__": 0, "default_quality": null, "ilumina_casava": false, "output_fmt_select": "fastqsanger", "output_quality": false}`
outputs	`"other"`
read_numbering	`""`

Step 9: MultiQC (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9507e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 20, "input": {"values": [{"id": 9, "src": "hdca"}]}, "software": "qualimap"}}]`
title	`"Host/Contamination Removal"`

Step 17: Invert Boolean (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 ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 0, "on_unmapped": "input"}`

Step 18: Reads with or without host-decontamination (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 37, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 5, "src": "dce"}]}}]}}`

Step 19: KMA (toolshed.g2.bx.psu.edu/repos/iuc/kma/kma_map/1.6.8+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kma_index	`None`
settings	`{"__current_case__": 0, "advanced": "simple"}`
single_paired	`{"__current_case__": 1, "input_sequences": {"values": [{"id": 38, "src": "dce"}]}, "single_paired_selector": "single"}`

Step 20: List of lists (__APPLY_RULES__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
input	`{"values": [{"id": 11, "src": "hdca"}]}`
rules	`{"mapping": [{"columns": [0, 1], "editing": false, "type": "list_identifiers"}], "rules": [{"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}]}`

Step 21: Optional pass 6 (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 41, "src": "dce"}]}}]}}`

Step 22: Canu (toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/2.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/canu:2.3--h3fb4750_2

Command Line:

canu -p canu -d ./out_dir correctedErrorRate=0.2 minReadLength=400 minOverlapLength=100 corOutCoverage=40 stopOnLowCoverage=10 contigFilter=' 2 0 1.0 0.5 5 '  genomeSize='11k' minThreads=${GALAXY_SLOTS:-4} maxThreads=${GALAXY_SLOTS:-4} redMemory=${GALAXY_MEMORY_MB:-6144}M redThreads=${GALAXY_SLOTS:-4} obtovlThreads=${GALAXY_SLOTS:-4} utgovlThreads=${GALAXY_SLOTS:-4} batThreads=${GALAXY_SLOTS:-4} batMemory=${GALAXY_MEMORY_MB:-6144}M cormhapMemory=${GALAXY_MEMORY_MB:-6144}M obtovlMemory=${GALAXY_MEMORY_MB:-6144}M utgovlMemory=${GALAXY_MEMORY_MB:-6144}M corThreads=${GALAXY_SLOTS:-4} corMemory=${GALAXY_MEMORY_MB:-6144}M cnsThreads=${GALAXY_SLOTS:-4} cnsMemory=${GALAXY_MEMORY_MB:-6144}M oeaMemory=${GALAXY_MEMORY_MB:-6144}M oeaThreads=${GALAXY_SLOTS:-4} merylThreads=${GALAXY_SLOTS:-4} merylMemory=${GALAXY_MEMORY_MB:-6144}M corovlThreads=${GALAXY_SLOTS:-4} corovlMemory=${GALAXY_MEMORY_MB:-6144}M useGrid=false   -nanopore -trimmed  '/tmp/tmpfplbed14/files/5/7/2/dataset_5720ef49-9a15-4aec-a665-891f960c3016.dat' 2>&1

Exit Code:

```
0
```

Standard Output:

-- canu master +27 changes (r10515 2a41e933b8de6ed66723d75d36dd071b46d2c347)
--
-- CITATIONS
--
-- For 'standard' assemblies of PacBio or Nanopore reads:
--   Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
--   Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
--   Genome Res. 2017 May;27(5):722-736.
--   http://doi.org/10.1101/gr.215087.116
-- 
-- Read and contig alignments during correction and consensus use:
--   Šošic M, Šikic M.
--   Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
--   Bioinformatics. 2017 May 1;33(9):1394-1395.
--   http://doi.org/10.1093/bioinformatics/btw753
-- 
-- Overlaps are generated using:
--   Berlin K, et al.
--   Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
--   Nat Biotechnol. 2015 Jun;33(6):623-30.
--   http://doi.org/10.1038/nbt.3238
-- 
--   Myers EW, et al.
--   A Whole-Genome Assembly of Drosophila.
--   Science. 2000 Mar 24;287(5461):2196-204.
--   http://doi.org/10.1126/science.287.5461.2196
-- 
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
--   Chin CS, et al.
--   Phased diploid genome assembly with single-molecule real-time sequencing.
--   Nat Methods. 2016 Dec;13(12):1050-1054.
--   http://doi.org/10.1038/nmeth.4035
-- 
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
--   Chin CS, et al.
--   Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
--   Nat Methods. 2013 Jun;10(6):563-9
--   http://doi.org/10.1038/nmeth.2474
-- 
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '23.0.2-internal' (from '/usr/local/lib/jvm/bin/java') without -d64 support.
-- Detected gnuplot version '5.4 patchlevel 10   ' (from 'gnuplot') and image format 'png'.
-- Detected samtools version '1.22.1' / htslib version 'htscodecs=1.6.4' (from 'samtools').
--
-- Detected 4 CPUs and 16 gigabytes of memory on the local machine.
--
-- Local machine mode enabled; grid support not detected or not allowed.
--
-- Found trimmed corrected Nanopore reads in the input files.
--
-- Job limits:
--      1 CPUs              (maxThreads option).
--
--                                (tag)Concurrency
--                         (tag)Threads          |
--                (tag)Memory         |          |
--        (tag)             |         |          |       total usage      algorithm
--        -------  ----------  --------   --------  --------------------  -----------------------------
-- Local: meryl      6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (k-mer counting)
-- Local: cormhap    6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (overlap detection with mhap)
-- Local: obtovl     6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (overlap detection)
-- Local: utgovl     6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (overlap detection)
-- Local: cor        6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (read correction)
-- Local: ovb        4.000 GB    1 CPU  x   1 job      4.000 GB   1 CPU   (overlap store bucketizer)
-- Local: ovs        8.000 GB    1 CPU  x   1 job      8.000 GB   1 CPU   (overlap store sorting)
-- Local: red        6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (read error detection)
-- Local: oea        6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (overlap error adjustment)
-- Local: bat        6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (contig construction with bogart)
-- Local: cns        6.000 GB    1 CPU  x   1 job      6.000 GB   1 CPU   (consensus)
--
-- Generating assembly 'canu' in '/tmp/tmpfplbed14/job_working_directory/000/21/working/out_dir':
--   genomeSize:
--     11000
--
--   Overlap Generation Limits:
--     corOvlErrorRate 0.3200 ( 32.00%)
--     obtOvlErrorRate 0.2000 ( 20.00%)
--     utgOvlErrorRate 0.2000 ( 20.00%)
--
--   Overlap Processing Limits:
--     corErrorRate    0.3000 ( 30.00%)
--     obtErrorRate    0.2000 ( 20.00%)
--     utgErrorRate    0.2000 ( 20.00%)
--     cnsErrorRate    0.2000 ( 20.00%)
--
--   Stages to run:
--     assemble corrected and trimmed reads.
--
--
-- BEGIN STORE CREATION
----------------------------------------
-- Starting command on Thu Feb 12 08:04:18 2026 with 32.473 GB free disk space

    cd .
    ./canu.seqStore.sh \
    > ./canu.seqStore.err 2>&1

-- Finished on Thu Feb 12 08:04:19 2026 (one second) with 32.459 GB free disk space
----------------------------------------
--
-- In sequence store './canu.seqStore':
--   Found 1435 reads.
--   Found 2200765 bases (200.06 times coverage).
--    Histogram of corrected reads:
--    
--    G=2200765                          sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010         1939       100       220238  ||        400-484            22|----
--    00020         1891       216       441935  ||        485-569            15|---
--    00030         1852       333       660980  ||        570-654             4|-
--    00040         1553       456       880970  ||        655-739            10|--
--    00050         1476       603      1101658  ||        740-824            12|--
--    00060         1453       753      1321173  ||        825-909             7|--
--    00070         1419       906      1540748  ||        910-994             2|-
--    00080         1383      1063      1760913  ||        995-1079           15|---
--    00090         1335      1225      1981284  ||       1080-1164            4|-
--    00100          400      1435      2200765  ||       1165-1249           10|--
--    001.000x                1435      2200765  ||       1250-1334          107|-----------------
--                                               ||       1335-1419          322|----------------------------------------------------
--                                               ||       1420-1504          397|---------------------------------------------------------------
--                                               ||       1505-1589           61|----------
--                                               ||       1590-1674            2|-
--                                               ||       1675-1759           13|---
--                                               ||       1760-1844           77|-------------
--                                               ||       1845-1929          236|--------------------------------------
--                                               ||       1930-2014           59|----------
--                                               ||       2015-2099            4|-
--                                               ||       2100-2184            5|-
--                                               ||       2185-2269           11|--
--                                               ||       2270-2354           13|---
--                                               ||       2355-2439           21|----
--                                               ||       2440-2524            2|-
--                                               ||       2525-2609            0|
--                                               ||       2610-2694            0|
--                                               ||       2695-2779            1|-
--                                               ||       2780-2864            0|
--                                               ||       2865-2949            0|
--                                               ||       2950-3034            0|
--                                               ||       3035-3119            0|
--                                               ||       3120-3204            1|-
--                                               ||       3205-3289            1|-
--                                               ||       3290-3374            0|
--                                               ||       3375-3459            0|
--                                               ||       3460-3544            0|
--                                               ||       3545-3629            0|
--                                               ||       3630-3714            0|
--                                               ||       3715-3799            1|-
--    
--
-- In sequence store './canu.seqStore':
--   Found 1435 reads.
--   Found 2200765 bases (200.06 times coverage).
--    Histogram of corrected-trimmed reads:
--    
--    G=2200765                          sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010         1939       100       220238  ||        400-484            22|----
--    00020         1891       216       441935  ||        485-569            15|---
--    00030         1852       333       660980  ||        570-654             4|-
--    00040         1553       456       880970  ||        655-739            10|--
--    00050         1476       603      1101658  ||        740-824            12|--
--    00060         1453       753      1321173  ||        825-909             7|--
--    00070         1419       906      1540748  ||        910-994             2|-
--    00080         1383      1063      1760913  ||        995-1079           15|---
--    00090         1335      1225      1981284  ||       1080-1164            4|-
--    00100          400      1435      2200765  ||       1165-1249           10|--
--    001.000x                1435      2200765  ||       1250-1334          107|-----------------
--                                               ||       1335-1419          322|----------------------------------------------------
--                                               ||       1420-1504          397|---------------------------------------------------------------
--                                               ||       1505-1589           61|----------
--                                               ||       1590-1674            2|-
--                                               ||       1675-1759           13|---
--                                               ||       1760-1844           77|-------------
--                                               ||       1845-1929          236|--------------------------------------
--                                               ||       1930-2014           59|----------
--                                               ||       2015-2099            4|-
--                                               ||       2100-2184            5|-
--                                               ||       2185-2269           11|--
--                                               ||       2270-2354           13|---
--                                               ||       2355-2439           21|----
--                                               ||       2440-2524            2|-
--                                               ||       2525-2609            0|
--                                               ||       2610-2694            0|
--                                               ||       2695-2779            1|-
--                                               ||       2780-2864            0|
--                                               ||       2865-2949            0|
--                                               ||       2950-3034            0|
--                                               ||       3035-3119            0|
--                                               ||       3120-3204            1|-
--                                               ||       3205-3289            1|-
--                                               ||       3290-3374            0|
--                                               ||       3375-3459            0|
--                                               ||       3460-3544            0|
--                                               ||       3545-3629            0|
--                                               ||       3630-3714            0|
--                                               ||       3715-3799            1|-
--    
--
-- Correction skipped; not enabled.
--
-- Trimming skipped; not enabled.
--
-- BEGIN ASSEMBLY
----------------------------------------
-- Starting command on Thu Feb 12 08:04:19 2026 with 32.459 GB free disk space

    cd unitigging/0-mercounts
    ./meryl-configure.sh \
    > ./meryl-configure.err 2>&1

-- Finished on Thu Feb 12 08:04:19 2026 (like a bat out of hell) with 32.459 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--        01  0.01 GB       2
--        02  -.-- GB       -  (segment size too small)
--        04  -.-- GB       -  (segment size too small)
--        06  -.-- GB       -  (segment size too small)
--        08  -.-- GB       -  (segment size too small)
--        12  -.-- GB       -  (segment size too small)
--        16  -.-- GB       -  (segment size too small)
--        20  -.-- GB       -  (segment size too small)
--        24  -.-- GB       -  (segment size too small)
--        32  -.-- GB       -  (segment size too small)
--        40  -.-- GB       -  (segment size too small)
--        48  -.-- GB       -  (segment size too small)
--        56  -.-- GB       -  (segment size too small)
--        64  -.-- GB       -  (segment size too small)
--        96  -.-- GB       -  (segment size too small)
--
--  For 1435 reads with 2200765 bases, limit to 1 batch.
--  Will count kmers using 01 jobs, each using 2 GB and 1 threads.
--
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Feb 12 08:04:19 2026 with 32.459 GB free disk space (1 processes; 1 concurrently)

    cd unitigging/0-mercounts
    ./meryl-count.sh 1 > ./meryl-count.000001.out 2>&1

-- Finished on Thu Feb 12 08:04:20 2026 (one second) with 32.447 GB free disk space
----------------------------------------
-- Found 1 Kmer counting (meryl) outputs.
-- Finished stage 'utg-merylCountCheck', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Feb 12 08:04:20 2026 with 32.447 GB free disk space (1 processes; 1 concurrently)

    cd unitigging/0-mercounts
    ./meryl-process.sh 1 > ./meryl-process.000001.out 2>&1

-- Finished on Thu Feb 12 08:04:21 2026 (one second) with 32.457 GB free disk space
----------------------------------------
-- Meryl finished successfully.  Kmer frequency histogram:
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2     67289 ********************************************************************** 0.5250 0.2019
--       3-     4     32260 *********************************                                      0.6947 0.2998
--       5-     7     12649 *************                                                          0.8238 0.4081
--       8-    11      6017 ******                                                                 0.8912 0.4961
--      12-    16      3438 ***                                                                    0.9290 0.5704
--      17-    22      2178 **                                                                     0.9527 0.6377
--      23-    29      1293 *                                                                      0.9680 0.6969
--      30-    37       938                                                                        0.9771 0.7435
--      38-    46       570                                                                        0.9841 0.7891
--      47-    56       423                                      
..
875 reads have no best edges (singleton)
--        20 reads have only one best edge (spur) 
--                 15 are mutual best
--         9 reads have two best edges 
--                  1 have one mutual best edge
--                  7 have two mutual best edges
--  
--  
--  FINAL EDGES
--  -------- ----------------------------------------
--       210 reads are contained
--     21875 reads have no best edges (singleton)
--        20 reads have only one best edge (spur) 
--                 15 are mutual best
--         9 reads have two best edges 
--                  1 have one mutual best edge
--                  7 have two mutual best edges
--  
--  
--  EDGE FILTERING
--  -------- ------------------------------------------
--         0 reads are ignored
--       393 reads have a gap in overlap coverage
--         0 reads have lopsided best edges
-- Found, in version 1, after unitig construction:
--   contigs:      3 sequences, total length 5868 bp (including 0 repeats of total length 0 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  1365 sequences, total length 2094380 bp.
--
-- Contig sizes based on genome size 11kbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10        1976             1        1976
--     20        1968             2        3944
--     30        1968             2        3944
--     40        1924             3        5868
--     50        1924             3        5868
--
-- Finished stage 'unitigCheck', reset canuIteration.
----------------------------------------
-- Starting command on Thu Feb 12 08:07:32 2026 with 32.441 GB free disk space

    cd unitigging
    /usr/local/bin/utgcns \
      -S ../canu.seqStore \
      -T  ./canu.ctgStore 1 \
      -partition 0.8 1 0.1 \
    > ./canu.ctgStore/partitioning.log 2>&1

-- Finished on Thu Feb 12 08:07:32 2026 (in the blink of an eye) with 32.44 GB free disk space
----------------------------------------
-- Using slow alignment for consensus (iteration '0').
-- Configured 22 consensus jobs.
-- Finished stage 'consensusConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'cns' concurrent execution on Thu Feb 12 08:07:32 2026 with 32.44 GB free disk space (22 processes; 1 concurrently)

    cd unitigging/5-consensus
    ./consensus.sh 1 > ./consensus.000001.out 2>&1
    ./consensus.sh 2 > ./consensus.000002.out 2>&1
    ./consensus.sh 3 > ./consensus.000003.out 2>&1
    ./consensus.sh 4 > ./consensus.000004.out 2>&1
    ./consensus.sh 5 > ./consensus.000005.out 2>&1
    ./consensus.sh 6 > ./consensus.000006.out 2>&1
    ./consensus.sh 7 > ./consensus.000007.out 2>&1
    ./consensus.sh 8 > ./consensus.000008.out 2>&1
    ./consensus.sh 9 > ./consensus.000009.out 2>&1
    ./consensus.sh 10 > ./consensus.000010.out 2>&1
    ./consensus.sh 11 > ./consensus.000011.out 2>&1
    ./consensus.sh 12 > ./consensus.000012.out 2>&1
    ./consensus.sh 13 > ./consensus.000013.out 2>&1
    ./consensus.sh 14 > ./consensus.000014.out 2>&1
    ./consensus.sh 15 > ./consensus.000015.out 2>&1
    ./consensus.sh 16 > ./consensus.000016.out 2>&1
    ./consensus.sh 17 > ./consensus.000017.out 2>&1
    ./consensus.sh 18 > ./consensus.000018.out 2>&1
    ./consensus.sh 19 > ./consensus.000019.out 2>&1
    ./consensus.sh 20 > ./consensus.000020.out 2>&1
    ./consensus.sh 21 > ./consensus.000021.out 2>&1
    ./consensus.sh 22 > ./consensus.000022.out 2>&1

-- Finished on Thu Feb 12 08:07:37 2026 (5 seconds) with 32.436 GB free disk space
----------------------------------------
-- Using slow alignment for consensus (iteration '1').
-- Configured 22 consensus jobs.
-- All 22 consensus jobs finished successfully.
-- Finished stage 'consensusCheck', reset canuIteration.
-- Using slow alignment for consensus (iteration '0').
-- Configured 22 consensus jobs.
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.436 GB free disk space

    cd unitigging
    /usr/local/bin/tgStoreLoad \
      -S ../canu.seqStore \
      -T  ./canu.ctgStore 2 \
      -L ./5-consensus/ctgcns.files \
    > ./5-consensus/ctgcns.files.ctgStoreLoad.err 2>&1

-- Finished on Thu Feb 12 08:07:37 2026 (lickety-split) with 32.432 GB free disk space
----------------------------------------
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.432 GB free disk space

    cd unitigging
    /usr/local/bin/tgTigDisplay \
      -S ../canu.seqStore \
      -b \
      -o ../canu.contigs.unsorted.bam \
      -L ./5-consensus/ctgcns.files \
    > ./5-consensus/ctgcns.files.contigs.bam.err 2>&1

-- Finished on Thu Feb 12 08:07:37 2026 (in the blink of an eye) with 32.431 GB free disk space
----------------------------------------
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.431 GB free disk space

    cd .
    samtools sort \
      --write-index \
      --threads 2 \
      -o ./canu.contigs.bam ./canu.contigs.unsorted.bam \
    > ./ctgcns.bam.err 2>&1

-- Finished on Thu Feb 12 08:07:37 2026 (fast as lightning) with 32.431 GB free disk space
----------------------------------------
-- Purging consensus output after loading to ctgStore.
-- Purged 22 .cns outputs.
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.435 GB free disk space

    cd unitigging
    /usr/local/bin/tgStoreDump \
      -S ../canu.seqStore \
      -T ./canu.ctgStore 2 \
      -sizes -s 11000 \
    > ./canu.ctgStore/seqDB.v002.sizes.txt
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.

-- Finished on Thu Feb 12 08:07:37 2026 (in the blink of an eye) with 32.435 GB free disk space
----------------------------------------
-- Found, in version 2, after consensus generation:
--   contigs:      3 sequences, total length 5720 bp (including 0 repeats of total length 0 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  1365 sequences, total length 2094194 bp.
--
-- Contig sizes based on genome size 11kbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10        1973             1        1973
--     20        1901             2        3874
--     30        1901             2        3874
--     40        1846             3        5720
--     50        1846             3        5720
--
-- Finished stage 'consensusLoad', reset canuIteration.
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.435 GB free disk space

    cd .
    /usr/local/bin/tgStoreDump \
      -S ./canu.seqStore \
      -T ./unitigging/canu.ctgStore 2 \
      -o ./canu.contigs \
      -layout \
    > ./canu.contigs.layout.err 2>&1

-- Finished on Thu Feb 12 08:07:37 2026 (furiously fast) with 32.435 GB free disk space
----------------------------------------
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.435 GB free disk space

    cd .
    /usr/local/bin/tgStoreDump \
      -S ./canu.seqStore \
      -T ./unitigging/canu.ctgStore 2 \
      -consensus -fasta \
      -unassembled \
    > ./canu.unassembled.fasta
    2> ./canu.unassembled.err
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.

-- Finished on Thu Feb 12 08:07:37 2026 (lickety-split) with 32.433 GB free disk space
----------------------------------------
----------------------------------------
-- Starting command on Thu Feb 12 08:07:37 2026 with 32.433 GB free disk space

    cd .
    /usr/local/bin/tgStoreDump \
      -S ./canu.seqStore \
      -T ./unitigging/canu.ctgStore 2 \
      -consensus -fasta \
      -contigs \
    > ./canu.contigs.fasta
    2> ./canu.contigs.err
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.

-- Finished on Thu Feb 12 08:07:37 2026 (lickety-split) with 32.433 GB free disk space
----------------------------------------
-- Finished stage 'generateOutputs', reset canuIteration.
--
-- Assembly 'canu' finished in '/tmp/tmpfplbed14/job_working_directory/000/21/working/out_dir'.
--
-- Summary saved in 'canu.report'.
--
-- Sequences saved:
--   Contigs       -> 'canu.contigs.fasta'
--   Unassembled   -> 'canu.unassembled.fasta'
--
-- Read layouts saved:
--   Contigs       -> 'canu.contigs.layout'.
--
-- Bye.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contigFilter	`{"lowCovDepth": "5", "lowCovSpan": "0.5", "minLength": "0", "minReads": "2", "singleReadSpan": "1.0"}`
corOutCoverage	`"40"`
correctedErrorRate	`"0.2"`
dbkey	`"?"`
genomeSize	`"11k"`
haplotypes	`[]`
minInputCoverage	`None`
minOverlapLength	`"100"`
minReadLength	`"400"`
processing	`"-trimmed"`
rawErrorRate	`None`
s	`None`
stage	`"all"`
stopOnLowCoverage	`"10"`
technology	`"-nanopore"`

Step 23: Kraken2 (toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.17.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.0"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"__current_case__": 0, "create_report": "true", "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 1, "input_sequences": {"values": [{"id": 46, "src": "dce"}]}, "single_paired_selector": "no"}`
split_reads	`false`
use_names	`false`

Step 24: Pass Conditional 2 (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 48, "src": "dce"}]}}]}}`

Step 25: Optional pass 7 (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 53, "src": "dce"}]}}]}}`

Step 26: Best Organism - hybrid assembly:

step_state: scheduled

Subworkflow Steps

Step 1: Nucleotide query sequence(s):
- step_state: scheduled
Step 2: Blast Database:
- step_state: scheduled

Step 3: Blastn (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.16.0+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/blast:2.16.0--h66d330f_5

Command Line:

blastn  -query '/tmp/tmpfplbed14/files/c/8/2/dataset_c826b92f-aa14-490c-8fa7-3a48b637884a.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/blastdb/nt/2023-09-01/nt"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmpfplbed14/job_working_directory/000/27/outputs/dataset_20b4a9a2-eb7b-4630-a92e-ef49f4d411ec.dat' -outfmt '6 qseqid bitscore sacc stitle'  -num_threads "${GALAXY_SLOTS:-8}" -strand both -dust yes

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
adv_opts	`{"__current_case__": 1, "adv_optional_id_files_opts": {"__current_case__": 0, "adv_optional_id_files_opts_selector": "none"}, "adv_opts_selector": "advanced", "filter_query": true, "gapextend": null, "gapopen": null, "identity_cutoff": "0.0", "max_hits": "0", "max_hsps": null, "parse_deflines": false, "qcov_hsp_perc": "0.0", "strand": "-strand both", "ungapped": false, "window_size": null, "word_size": null}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": "nt_2023-09-01", "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": null, "ids_cols": ["sacc", "stitle"], "misc_cols": null, "out_format": "cols", "std_cols": ["qseqid", "bitscore"], "tax_cols": null}`

Step 4: Sort (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-3b62966bb5abb1228683819650478f85a768a305:d811e96fbcf8ecf6b62f09be04e8ab2bae37af16-0

Command Line:

( export LC_ALL=C;  sort   --stable -t '	'  -k '2rn,2'  ) < '/tmp/tmpfplbed14/files/2/0/b/dataset_20b4a9a2-eb7b-4630-a92e-ef49f4d411ec.dat' > '/tmp/tmpfplbed14/job_working_directory/000/28/outputs/dataset_3c403626-e2ca-4658-9653-c86673b66725.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "2", "order": "r", "style": "n"}]`
unique	`false`

Step 5: Cut (Cut1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/perl:5.26--2
```

Command Line:

perl '/tmp/tmpfplbed14/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpfplbed14/files/3/c/4/dataset_3c403626-e2ca-4658-9653-c86673b66725.dat' 'c3' T '/tmp/tmpfplbed14/job_working_directory/000/29/outputs/dataset_00b0a5fc-d3b8-49e5-aa94-76f1516b3e27.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 6: Best 5 Hits (Show beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

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

Command Line:

head -n 5 '/tmp/tmpfplbed14/files/0/0/b/dataset_00b0a5fc-d3b8-49e5-aa94-76f1516b3e27.dat' > '/tmp/tmpfplbed14/job_working_directory/000/30/outputs/dataset_73ff105e-fce8-4f67-9bc4-66554203e9a5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"5"`

Step 7: Best Hit (Show beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

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

Command Line:

head -n 1 '/tmp/tmpfplbed14/files/0/0/b/dataset_00b0a5fc-d3b8-49e5-aa94-76f1516b3e27.dat' > '/tmp/tmpfplbed14/job_working_directory/000/31/outputs/dataset_edfcb85f-9745-449e-9d4e-4eb0d29e46f9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Step 8: Get Data 2 (toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/ncbi-acc-download:0.2.8--pyh5e36f6f_0

Command Line:

{ grep -v "^[ \t]*$" /tmp/tmpfplbed14/files/7/3/f/dataset_73ff105e-fce8-4f67-9bc4-66554203e9a5.dat > accessions || { echo "No accession numbers in input. Aborting." 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=1 && while read accession; do echo "Downloading accession number: " $accession " ..." >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo " failed." >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo " done." >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ignore_failed	`"1"`
molecule	`{"__current_case__": 0, "format": "fasta", "select": "nucleotide"}`
query_source	`{"__current_case__": 0, "accession_file": {"values": [{"id": 60, "src": "dce"}]}, "select": "accession_file"}`
range	`None`

Step 9: Get Data (toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/ncbi-acc-download:0.2.8--pyh5e36f6f_0

Command Line:

{ grep -v "^[ \t]*$" /tmp/tmpfplbed14/files/e/d/f/dataset_edfcb85f-9745-449e-9d4e-4eb0d29e46f9.dat > accessions || { echo "No accession numbers in input. Aborting." 1>&2; exit 1; } } && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo "Downloading accession number: " $accession " ..." >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo " failed." >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo " done." >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ignore_failed	`"0"`
molecule	`{"__current_case__": 0, "format": "fasta", "select": "nucleotide"}`
query_source	`{"__current_case__": 0, "accession_file": {"values": [{"id": 61, "src": "dce"}]}, "select": "accession_file"}`
range	`None`

Step 10: Collapse Collection (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.1.0--2
```

Command Line:

(   cat "/tmp/tmpfplbed14/files/d/e/0/dataset_de085f69-d633-45f6-a33a-395144522350.dat" ;   cat "/tmp/tmpfplbed14/files/1/f/2/dataset_1f2d102f-1f9b-450a-abe7-65967c6081d4.dat" ;   cat "/tmp/tmpfplbed14/files/b/2/8/dataset_b2866344-1ce3-43cb-ae30-51d45560ae41.dat" ;   cat "/tmp/tmpfplbed14/files/7/7/2/dataset_772e871d-7c7d-486f-be42-7e253a868db3.dat" ;   cat "/tmp/tmpfplbed14/files/0/2/3/dataset_0230bcef-247f-4bc5-a681-30d7b672a6a8.dat" ;   ) > /tmp/tmpfplbed14/job_working_directory/000/35/outputs/dataset_2bf06beb-c8a4-4b30-9d0d-30e6b598277b.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 11: Collapse Collection 2 (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/gawk:5.1.0--2
```

Command Line:

(   cat "/tmp/tmpfplbed14/files/f/9/e/dataset_f9e64a44-e2d4-4d3c-ac03-02d9321aec4a.dat" ;   ) > /tmp/tmpfplbed14/job_working_directory/000/34/outputs/dataset_27a7bc65-d78a-4a5f-8a84-3b108031641b.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9607e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 27: Keaken to Krona (toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/krakentools:1.2.1--pyh7e72e81_0

Command Line:

kreport2krona.py --report '/tmp/tmpfplbed14/files/1/e/f/dataset_1eff6869-be23-41b7-8965-0dcf09e498cb.dat' --output '/tmp/tmpfplbed14/job_working_directory/000/25/outputs/dataset_cd8a5a47-1143-49c8-9b96-07c05c6199db.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
intermediate_ranks	`false`

Step 28: Select Reference (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": {"values": [{"id": 68, "src": "dce"}]}}]}}`

Step 29: Krona (toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
combine_inputs	`false`
dbkey	`"?"`
root_name	`"Root"`
type_of_data	`{"__current_case__": 1, "input": {"values": [{"id": 28, "src": "hdca"}]}, "type_of_data_selector": "text"}`

Step 30: Minimap2 (toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3a70f8bc7e17b723591f6132418640cfdbc88246-0

Command Line:

ln -f -s '/tmp/tmpfplbed14/files/2/7/a/dataset_27a7bc65-d78a-4a5f-8a84-3b108031641b.dat' reference.fa && minimap2 -x map-ont    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpfplbed14/files/5/7/2/dataset_5720ef49-9a15-4aec-a665-891f960c3016.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpfplbed14/job_working_directory/000/37/outputs/dataset_e21aba09-f685-46f3-9b80-58282c417cd5.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.002*1.47] collected minimizers
[M::mm_idx_gen::0.003*1.33] sorted minimizers
[M::main::0.003*1.33] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.003*1.31] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.003*1.29] distinct minimizers: 3578 (99.94% are singletons); average occurrences: 1.001; average spacing: 5.290; total length: 18937
[M::worker_pipeline::9.886*0.95] mapped 22364 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x map-ont --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpfplbed14/files/5/7/2/dataset_5720ef49-9a15-4aec-a665-891f960c3016.dat
[M::main] Real time: 9.899 sec; CPU: 9.436 sec; Peak RSS: 0.104 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "map-ont", "fastq_input1": {"values": [{"id": 38, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 75, "src": "dce"}]}, "reference_source_selector": "history"}`

Step 31: Samtools consensus (toolshed.g2.bx.psu.edu/repos/iuc/samtools_consensus/samtools_consensus/1.22+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/samtools:1.22--h96c455f_0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&        ln -s '/tmp/tmpfplbed14/files/e/2/1/dataset_e21aba09-f685-46f3-9b80-58282c417cd5.dat' infile && ln -s '/tmp/tmpfplbed14/files/_metadata_files/8/9/a/metadata_89af1a3f-2ac8-4e30-a918-7708f9a0da32.dat' infile.bai &&   samtools consensus infile -f 'fasta' -@ $addthreads  --min-MQ 0 --min-BQ 0      --rf 0 --ff 0  -m 'bayesian' -C 10 --use-MQ --adj-MQ --NM-halo 50 --low-MQ 1 --high-MQ 60 --scale-MQ 1.0 --P-het 0.001 --P-indel 0.0002 --het-scale 1.0   --min-depth 1      -l 70  --show-del no --show-ins yes   > /tmp/tmpfplbed14/job_working_directory/000/38/outputs/dataset_5ee75a08-85a3-49e4-90ac-02e41769e1aa.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
consensus_options	`{"__current_case__": 1, "mode": "bayesian", "settings": {"config_cond": {"C": "10", "__current_case__": 0, "calibration_cond": {"__current_case__": 5, "calibration_file": null, "calibration_param": "file"}, "config_param": "manual", "hetero_scale": "1.0", "hom_fix": false, "hom_score": null, "mq_cond": {"__current_case__": 0, "adj_mq": true, "high_mq": "60", "low_mq": "1", "mismatch_window": "50", "mq_param": "--use-MQ", "scale_mq": "1.0"}, "p_het": "0.001", "p_indel": "0.0002"}}}`
dbkey	`"?"`
format	`"fasta"`
global_settings	`{"addref_cond": {"__current_case__": 0, "addref_select": "no"}, "minimum_depth": "1", "reg_repeat": []}`
output_options	`{"all": false, "ambig": false, "line_len": "70", "mark_insertions": false, "show_deletions": false, "show_insertions": true}`
preprocessing_options	`{"exclusive_filter": null, "inclusive_filter": null, "minimum_BQ": "0", "minimum_MQ": "0"}`

Step 32: Mapping Quality (toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/qualimap:2.3--hdfd78af_0

Command Line:

export JAVA_OPTS="-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m" &&    ln -s '/tmp/tmpfplbed14/files/e/2/1/dataset_e21aba09-f685-46f3-9b80-58282c417cd5.dat' 'ERR1248114' &&  qualimap bamqc -bam 'ERR1248114' -outdir results -outformat html --collect-overlap-pairs -nw 400  -hm 3  -nt ${GALAXY_SLOTS:-1} &&   sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/tmp/tmpfplbed14/job_working_directory/000/39/outputs/dataset_c0a6136b-8264-48fc-9235-b98b8399f10f.dat' && mkdir '/tmp/tmpfplbed14/job_working_directory/000/39/outputs/dataset_c0a6136b-8264-48fc-9235-b98b8399f10f_files' && mv results/css/*.css '/tmp/tmpfplbed14/job_working_directory/000/39/outputs/dataset_c0a6136b-8264-48fc-9235-b98b8399f10f_files' && mv results/css/*.png '/tmp/tmpfplbed14/job_working_directory/000/39/outputs/dataset_c0a6136b-8264-48fc-9235-b98b8399f10f_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/tmp/tmpfplbed14/job_working_directory/000/39/outputs/dataset_c0a6136b-8264-48fc-9235-b98b8399f10f_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv "results/raw_data_qualimapReport/$file" `echo "results/$file" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt

Exit Code:

```
0
```

Standard Output:

Java memory size is set to 1200M
Launching application...

detected environment java options -Djava.awt.headless=true -Xmx1024m
QualiMap v.2.3
Built on 2023-05-19 16:57

Selected tool: bamqc
Available memory (Mb): 253
Max memory (Mb): 1037
Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Number of windows: 400, effective number of windows: 395
Chunk of reads size: 1000
Number of threads: 1
Processed 50 out of 395 windows...
Processed 100 out of 395 windows...
Processed 150 out of 395 windows...
Processed 200 out of 395 windows...
Processed 250 out of 395 windows...
Processed 300 out of 395 windows...
Processed 350 out of 395 windows...
Total processed windows:395
Number of reads: 22364
Number of valid reads: 22227
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 22168
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 7
Computing descriptors...
numberOfMappedBases: 32955797
referenceSize: 18937
numberOfSequencedBases: 30459854
numberOfAs: 8834608
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 8
end of bam qc
Computing report...
Writing HTML report...
HTML report created successfully

Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicate_skipping	`None`
per_base_coverage	`false`
plot_specific	`{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": false}`
stats_regions	`{"__current_case__": 0, "region_select": "all"}`

Step 33: Rename:

step_state: scheduled

Subworkflow Steps

Step 1: Unlabelled step:
- step_state: scheduled

Step 2: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpfplbed14/job_working_directory/000/40/configs/tmp01uzgq1e' '/tmp/tmpfplbed14/job_working_directory/000/40/outputs/dataset_0d1887f2-bac0-4619-853c-1e3ced2b1051.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fce87a9707e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 43, "src": "hdca"}]}`

Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/python:3.5--2
```

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmpfplbed14/files/0/d/1/dataset_0d1887f2-bac0-4619-853c-1e3ced2b1051.dat' --ftype 'tabular' --top '0' --by 'row' --chunksize 1 --file_names 'split_file' --file_ext 'tabular'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"fce87a9707e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 0, "input": {"values": [{"id": 100, "src": "hda"}]}, "select_ftype": "tabular", "split_by": {"__current_case__": 1, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}, "select_split_by": "row"}, "top": "0"}`

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed -r --sandbox -e '' -e 's/^.*$/>&_consensus/g' '/tmp/tmpfplbed14/files/4/d/7/dataset_4d72d783-c821-4271-8744-556b26cc8175.dat' > '/tmp/tmpfplbed14/job_working_directory/000/43/outputs/dataset_79e85206-ac91-44f8-a57c-43de8a804353.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9707e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": "^.*$", "replace_pattern": ">&_consensus", "sed_options": null}]`

Step 5: Unlabelled step (param_value_from_file):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9707e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/sed:4.9
```

Command Line:

sed -r --sandbox -e '' -e 's/^>(.*)/>ERR1248114_consensus/g' '/tmp/tmpfplbed14/files/5/e/e/dataset_5ee75a08-85a3-49e4-90ac-02e41769e1aa.dat' > '/tmp/tmpfplbed14/job_working_directory/000/45/outputs/dataset_46a80a7e-1b95-496f-871a-1930765bc36f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9707e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": "^>(.*)", "replace_pattern": ">ERR1248114_consensus", "sed_options": null}]`

Step 34: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/2.5.2+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/sniffles:2.5.2--pyhdfd78af_0

Command Line:

ln -f -s '/tmp/tmpfplbed14/files/e/2/1/dataset_e21aba09-f685-46f3-9b80-58282c417cd5.dat' input.bam && ln -f -s '/tmp/tmpfplbed14/files/_metadata_files/8/9/a/metadata_89af1a3f-2ac8-4e30-a918-7708f9a0da32.dat' input.bam.bai && ln -f -s '/tmp/tmpfplbed14/files/5/e/e/dataset_5ee75a08-85a3-49e4-90ac-02e41769e1aa.dat' 'reference.fa' && sniffles -t ${GALAXY_SLOTS:-2} -i 'input.bam' -v '/tmp/tmpfplbed14/job_working_directory/000/42/outputs/dataset_e193ec3c-0dac-45fd-8f59-2dfb5af9a0ae.dat' --allow-overwrite --reference 'reference.fa' --minsupport 'auto' --max-splits-kb '0.1' --minsvlen '50' --mapq '20' --min-alignment-length '100' --cluster-binsize '100' --cluster-r '2.5'

Exit Code:

```
0
```

Standard Output:

2026-02-12 11:24:51,520 INFO sniffles.main (10): Running Sniffles2, build 2.5
2026-02-12 11:24:51,520 INFO sniffles.main (10):   Run Mode: call_sample
2026-02-12 11:24:51,520 INFO sniffles.main (10):   Start on: 2026/02/12 11:24:51
2026-02-12 11:24:51,520 INFO sniffles.main (10):   Working dir: /tmp/tmpfplbed14/job_working_directory/000/42/working
2026-02-12 11:24:51,521 INFO sniffles.main (10):   Used command: /usr/local/bin/sniffles -t 1 -i input.bam -v /tmp/tmpfplbed14/job_working_directory/000/42/outputs/dataset_e193ec3c-0dac-45fd-8f59-2dfb5af9a0ae.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5
2026-02-12 11:24:51,521 INFO sniffles.main (10): ==============================
2026-02-12 11:24:51,532 INFO sniffles.main (10): Opening for reading: input.bam
2026-02-12 11:24:51,534 INFO sniffles.main (10): Opening for reading: reference.fa
Info: Fasta index for reference.fa not found. Generating with pysam.faidx (this may take a while)
2026-02-12 11:24:51,535 INFO sniffles.main (10): Opening for writing: /tmp/tmpfplbed14/job_working_directory/000/42/outputs/dataset_e193ec3c-0dac-45fd-8f59-2dfb5af9a0ae.dat (single-sample, sorted)
2026-02-12 11:24:51,546 INFO sniffles.main (10): 
2026-02-12 11:24:51,546 INFO sniffles.main (10): Analyzing 22227 alignments total...
2026-02-12 11:24:51,546 INFO sniffles.main (10): 
2026-02-12 11:24:51,546 INFO sniffles.worker (10): Starting worker 0
2026-02-12 11:24:51,549 INFO sniffles.worker (10): Dispatched task #0 to worker 0 (0  tasks left)
2026-02-12 11:24:53,091 INFO sniffles.worker (10): Worker 0 got result for task #0
2026-02-12 11:24:53,192 INFO sniffles.worker (10): Worker 0 shutting down...
2026-02-12 11:24:53,200 INFO sniffles.worker (10): Worker 0 done (code 0).
2026-02-12 11:24:53,200 INFO sniffles.main (10): Took 1.65s.
2026-02-12 11:24:53,200 INFO sniffles.main (10): 
2026-02-12 11:24:53,201 INFO sniffles.main (10): Wrote 0 called SVs to /tmp/tmpfplbed14/job_working_directory/000/42/outputs/dataset_e193ec3c-0dac-45fd-8f59-2dfb5af9a0ae.dat (single-sample, sorted)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
advanced_options	`{"mosaic": false}`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
clustering_options	`{"clusterbinsize": "100", "clusterr": "2.5"}`
dbkey	`"?"`
general_options	`{"detectlargeins": true, "mapq": "20", "maxsplitskb": "0.1", "minalignmentlength": "100", "minsupport": "auto", "minsvlen": "50"}`
reference_genome	`{"__current_case__": 2, "genome": {"values": [{"id": 77, "src": "dce"}]}, "genome_type_select": "history"}`

Step 35: Best Organism - reference assembly:

step_state: scheduled

Subworkflow Steps

Step 1: Nucleotide query sequence(s):
- step_state: scheduled
Step 2: Blast Database:
- step_state: scheduled

Step 3: Blastn (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.16.0+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
adv_opts	`{"__current_case__": 1, "adv_optional_id_files_opts": {"__current_case__": 0, "adv_optional_id_files_opts_selector": "none"}, "adv_opts_selector": "advanced", "filter_query": true, "gapextend": null, "gapopen": null, "identity_cutoff": "0.0", "max_hits": "0", "max_hsps": null, "parse_deflines": false, "qcov_hsp_perc": "0.0", "strand": "-strand both", "ungapped": false, "window_size": null, "word_size": null}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": "nt_2023-09-01", "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": null, "ids_cols": ["sacc", "stitle"], "misc_cols": null, "out_format": "cols", "std_cols": ["qseqid", "bitscore"], "tax_cols": null}`

Step 4: Sort (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`"0"`
ignore_case	`false`
sortkeys	`[{"__index__": 0, "column": "2", "order": "r", "style": "n"}]`
unique	`false`

Step 5: Cut (Cut1):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 6: Best 5 Hits (Show beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"5"`

Step 7: Best Hit (Show beginning1):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`false`
lineNum	`"1"`

Step 8: Get Data 2 (toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ignore_failed	`"1"`
molecule	`{"__current_case__": 0, "format": "fasta", "select": "nucleotide"}`
query_source	`{"__current_case__": 0, "accession_file": {"values": [{"id": 101, "src": "dce"}]}, "select": "accession_file"}`
range	`None`

Step 9: Get Data (toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
ignore_failed	`"0"`
molecule	`{"__current_case__": 0, "format": "fasta", "select": "nucleotide"}`
query_source	`{"__current_case__": 0, "accession_file": {"values": [{"id": 102, "src": "dce"}]}, "select": "accession_file"}`
range	`None`

Step 10: Collapse Collection (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
input_list	`{"values": [{"id": 103, "src": "dce"}]}`
one_header	`false`

Step 11: Collapse Collection 2 (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9807e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
input_list	`{"values": [{"id": 106, "src": "dce"}]}`
one_header	`false`

Step 36: Which Blast Step? (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 74, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 108, "src": "dce"}]}}]}}`

Step 37: MAFFT (toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-027f30e88c6da4ab4b0170ff590dbab158b07243:43ff19c348e21674cd51004463f1ea0b2e5f2336-0

Command Line:

bash inputs.sh &&     mafft-fftns   --nuc  --kimura 200  --ep 0.0 --op 1.53       --thread ${GALAXY_SLOTS:-1} --threadit 0  input.fa > '/tmp/tmpfplbed14/job_working_directory/000/56/outputs/dataset_d544939f-984e-46a8-af8b-fd0d1d318f64.dat'

Exit Code:

```
0
```

Standard Error:

nthread = 1
nthreadpair = 1
nthreadtb = 1
jtt/kimura 200
ppenalty_ex = 0
stacksize: 16384 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..

There are 93 ambiguous characters.

    1 / 6 (thread    0)
done.

Constructing a UPGMA tree (efffree=0) ... 

    0 / 6
done.

Progressive alignment 1/2... 

STEP     1 / 5 (thread    0) f��
STEP     2 / 5 (thread    0) f��
STEP     3 / 5 (thread    0) f��
STEP     4 / 5 (thread    0) f��
STEP     5 / 5 (thread    0) f��
done.

Making a distance matrix from msa.. 

    0 / 6 (thread    0)
done.

Constructing a UPGMA tree (efffree=1) ... 

    0 / 6
done.

Progressive alignment 2/2... 

STEP     1 / 5 (thread    0) f��
STEP     2 / 5 (thread    0) f��
STEP     3 / 5 (thread    0) f��
STEP     4 / 5 (thread    0) f��
STEP     5 / 5 (thread    0) f��
done.

disttbfast (nuc) Version 7.526
alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
1 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
anysymbol	`false`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
datatype_selection	`{"__current_case__": 1, "datatype": "--nuc", "fmodel": false, "gap_costs": {"__current_case__": 1, "ep": "0.0", "op": "1.53", "use_defaults": "no"}, "scoring_matrix": {"__current_case__": 0, "coefficient": "200", "type": "--kimura"}}`
dbkey	`"?"`
flavour	`{"__current_case__": 2, "type": "mafft-fftns"}`
input	`{"__current_case__": 1, "batches": [{"__index__": 0, "inputs": {"values": [{"id": 63, "src": "hdca"}]}}, {"__index__": 1, "inputs": {"values": [{"id": 50, "src": "hdca"}]}}], "mapping": "merge"}`
outputFormat	`""`
reorder	`false`
seed	`None`
treeout	`false`

Step 38: CIAlign (toolshed.g2.bx.psu.edu/repos/iuc/cialign/cialign/1.1.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/cialign:1.1.4--pyhca03a8a_0

Command Line:

CIAlign --infile '/tmp/tmpfplbed14/files/d/5/4/dataset_d544939f-984e-46a8-af8b-fd0d1d318f64.dat' --outfile_stem 'output'        --remove_insertions --insertion_min_size 3 --insertion_max_size 10000 --insertion_min_flank 5 --insertion_min_perc 0.05  --crop_ends --crop_ends_mingap_perc 0.1 --crop_ends_redefine_perc 0.1       --plot_input --plot_output    --plot_width 5 --plot_height 3 --plot_dpi 300 --plot_keep_numbers  --plot_identity_palette 'bone' --plot_identity_gap_col '#ffffff' --plot_similarity_palette 'bone' --plot_similarity_gap_col '#ffffff' --plot_sub_matrix_name 'NUC.4.4' --palette 'CBS'      --make_consensus --consensus_type 'majority_nongap' --consensus_keep_gaps                 --deduplicate_ids --duporder 'first'

Exit Code:

```
0
```

Standard Output:

Removing insertions
Removing gap only columns
Cropping ends
Removing gap only columns
Plotting mini alignment for input
Plotting mini alignment for output
Building consensus sequence

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
basic_options	`{"all": false, "clean": false, "interpret": false, "log_out": false, "visualise": false}`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cleaning_options	{"crop_divergent_cond": {"__current_case__": 1, "crop_divergent_param": "false"}, "crop_ends_cond": {"__current_case__": 0, "crop_ends_mingap_perc": "0.1", "crop_ends_param": "true", "crop_ends_redefine_perc": "0.1", "crop_ends_retain_seqs": [], "crop_ends_retain_strings": []}, "keep_gaponly": false, "remove_divergent_cond": {"__current_case__": 1, "remove_divergent_param": "false"}, "remove_insertions_cond": {"__current_case__": 0, "insertion_max_size": "10000", "insertion_min_flank": "5", "insertion_min_perc": "0.05", "insertion_min_size": "3", "remove_insertions_param": "true"}, "remove_short_cond": {"__current_case__": 1, "remove_short_param": "false"}, "retain_cond": {"__current_case__": 1, "retain_param": "false"}}
dbkey	`"?"`
editing_functions	`{"deduplicate_ids": true, "duporder": "first", "get_section_cond": {"__current_case__": 1, "get_section_param": "false"}, "replace_input_tu": false, "replace_input_ut": false, "replace_output_tu": false, "replace_output_ut": false, "unalign_input": false, "unalign_output": false}`
interpretation_options	{"consensus_sequences_cond": {"__current_case__": 0, "consensus_keep_gaps": true, "consensus_sequences_param": "true", "consensus_type": "majority_nongap"}, "position_matrices": {"matrices_settings": {"pwm_alphatype": "calc", "pwm_alphaval": "1", "pwm_end": null, "pwm_freqtype": "equal", "pwm_start": null}, "pwm_input": false, "pwm_output": false, "pwm_output_blamm": false, "pwm_output_meme": false}, "similarity_matrices": {"make_similarity_matrix_input": false, "make_similarity_matrix_output": false, "similarity_matrices_settings": {"make_simmatrix_dp": "4", "make_simmatrix_keepgaps": "0", "make_simmatrix_minoverlap": "1"}}}
visualisation_options	{"basic_visualisation_options": {"output_settings_cond": {"__current_case__": 0, "output_settings_param": "true", "palette": "CBS", "plot_dpi": "300", "plot_force_numbers": false, "plot_height": "3", "plot_identity_gap_col": "#ffffff", "plot_identity_palette": "bone", "plot_keep_numbers": true, "plot_similarity_gap_col": "#ffffff", "plot_similarity_palette": "bone", "plot_sub_matrix_name": "NUC.4.4", "plot_width": "5"}, "plot_consensus_identity": false, "plot_consensus_similarity": false, "plot_input": true, "plot_markup": false, "plot_output": true}, "sequence_logo_cond": {"__current_case__": 1, "sequence_logo_param": "false"}, "statistics_plots": {"plot_stats_input": false, "plot_stats_output": false, "stats_settings": {"plot_stats_colour": "#0000ff", "plot_stats_dpi": "300", "plot_stats_height": "3", "plot_stats_width": "5"}}}

Step 39: IQ-TREE (toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/iqtree:2.4.0--h503566f_0

Command Line:

iqtree --prefix PREF -T ${GALAXY_SLOTS:-10} --redo  -s '/tmp/tmpfplbed14/files/8/1/a/dataset_81a9849e-3521-468c-ba06-ad39e0c7af18.dat'  --seqtype DNA            -m ''    --msub 'nuclear'    --cmin '2'  --cmax '10'  --merit 'AIC'                     --ninit '100'  --ntop '20'  --nbest '5'  --nstop '100'   --radius '6'  --perturb '0.5'                    --sup-min '0.0'             --nmax '1000'  --nstep '100'  --bcor '0.99'  --beps '0.5'

Exit Code:

```
0
```

Standard Output:

IQ-TREE multicore version 2.4.0 for Linux x86 64-bit built Feb 12 2025
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong

Host:    db3ad70681ac (AVX2, FMA3, 15 GB RAM)
Command: iqtree --prefix PREF -T 1 --redo -s /tmp/tmpfplbed14/files/8/1/a/dataset_81a9849e-3521-468c-ba06-ad39e0c7af18.dat --seqtype DNA -m  --msub nuclear --cmin 2 --cmax 10 --merit AIC --ninit 100 --ntop 20 --nbest 5 --nstop 100 --radius 6 --perturb 0.5 --sup-min 0.0 --nmax 1000 --nstep 100 --bcor 0.99 --beps 0.5
Seed:    849462 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Feb 12 11:26:45 2026
Kernel:  AVX+FMA - 1 threads (4 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file /tmp/tmpfplbed14/files/8/1/a/dataset_81a9849e-3521-468c-ba06-ad39e0c7af18.dat ... Fasta format detected
Reading fasta file: done in 0.00220501 secs using 92.11% CPU
Alignment most likely contains DNA/RNA sequences
Alignment has 6 sequences with 18957 columns, 52 distinct patterns
12 parsimony-informative, 36 singleton sites, 18909 constant sites
                      Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 1.3506e-05 secs
   1  KY401672.1              0.13%    passed     99.59%
   2  MG572231.1              0.24%    passed     99.60%
   3  MG572234.1              0.00%    passed     99.52%
   4  MH121161.1              1.13%    passed     99.87%
   5  MH425138.1              0.11%    passed     99.50%
   6  ERR1248114_consensus    3.47%    passed     73.38%
****  TOTAL                   0.85%  0 sequences failed composition chi2 test (p-value<5%; df=3)


Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -26361.377
Optimal log-likelihood: -26361.367
Rate parameters:  A-C: 1.08997  A-G: 7.64222  A-T: 0.64950  C-G: 0.44558  C-T: 3.85686  G-T: 1.00000
Base frequencies:  A: 0.318  C: 0.214  G: 0.198  T: 0.269
Proportion of invariable sites: 0.499
Gamma shape alpha: 998.448
Parameters optimization took 1 rounds (0.001 sec)
Time for fast ML tree search: 0.006 seconds

NOTE: ModelFinder requires 0 MB RAM!
ModelFinder will test up to 484 DNA models (sample size: 18957 epsilon: 0.100) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  GTR+F         26361.331    17  52756.662    52756.694    52890.111
  2  GTR+F+I       26361.328    18  52758.656    52758.693    52899.955
  3  GTR+F+G4      26361.328    18  52758.655    52758.691    52899.954
  4  GTR+F+I+G4    26361.351    19  52760.702    52760.742    52909.850
  5  GTR+F+R2      26361.316    19  52760.631    52760.672    52909.780
  6  GTR+F+R3      26361.310    21  52764.620    52764.669    52929.468
 14  GTR+F+I+R2    26361.340    20  52762.680    52762.724    52919.679
 15  GTR+F+I+R3    26361.338    22  52766.676    52766.729    52939.374
 23  SYM           26702.734    14  53433.467    53433.490    53543.366
 24  SYM+I         26702.726    15  53435.452    53435.478    53553.201
 25  SYM+G4        26702.722    15  53435.445    53435.470    53553.194
 26  SYM+I+G4      26702.757    16  53437.513    53437.542    53563.112
 27  SYM+R2        26702.716    16  53437.432    53437.461    53563.031
 28  SYM+R3        26702.713    18  53441.425    53441.462    53582.724
 36  SYM+I+R2      26702.744    17  53439.489    53439.521    53572.938
 45  TVM+F         26363.366    16  52758.731    52758.760    52884.330
 46  TVM+F+I       26363.347    17  52760.694    52760.726    52894.143
 47  TVM+F+G4      26363.341    17  52760.682    52760.715    52894.131
 48  TVM+F+I+G4    26363.362    18  52762.725    52762.761    52904.023
 49  TVM+F+R2      26363.329    18  52762.658    52762.694    52903.957
 50  TVM+F+R3      26363.326    20  52766.651    52766.696    52923.650
 58  TVM+F+I+R2    26363.352    19  52764.704    52764.744    52913.853
 67  TVMe          26704.892    13  53435.785    53435.804    53537.834
 68  TVMe+I        26704.887    14  53437.774    53437.796    53547.673
 69  TVMe+G4       26704.878    14  53437.755    53437.778    53547.654
 70  TVMe+I+G4     26704.901    15  53439.803    53439.828    53557.552
 71  TVMe+R2       26704.861    15  53439.721    53439.747    53557.470
 72  TVMe+R3       26704.856    17  53443.712    53443.744    53577.161
 80  TVMe+I+R2     26704.883    16  53441.766    53441.794    53567.364
 89  TIM3+F        26361.701    15  52753.402    52753.427    52871.151
 90  TIM3+F+I      26361.673    16  52755.346    52755.374    52880.944
 91  TIM3+F+G4     26361.669    16  52755.339    52755.368    52880.938
 92  TIM3+F+I+G4   26361.669    17  52757.338    52757.370    52890.787
 93  TIM3+F+R2     26361.631    17  52757.262    52757.294    52890.711
 94  TIM3+F+R3     26361.628    19  52761.255    52761.295    52910.404
102  TIM3+F+I+R2   26361.657    18  52759.314    52759.350    52900.613
111  TIM3e         26703.214    12  53430.428    53430.445    53524.627
112  TIM3e+I       26703.214    13  53432.428    53432.447    53534.477
113  TIM3e+G4      26703.213    13  53432.426    53432.445    53534.475
114  TIM3e+I+G4    26703.248    14  53434.497    53434.519    53544.396
115  TIM3e+R2      26703.212    14  53434.425    53434.447    53544.324
116  TIM3e+R3      26703.212    16  53438.425    53438.453    53564.023
124  TIM3e+I+R2    26703.248    15  53436.495    53436.521    53554.244
133  TIM2+F        26361.634    15  52753.269    52753.294    52871.017
134  TIM2+F+I      26361.629    16  52755.257    52755.286    52880.856
135  TIM2+F+G4     26361.622    16  52755.245    52755.274    52880.844
136  TIM2+F+I+G4   26361.649    17  52757.299    52757.331    52890.748
137  TIM2+F+R2     26361.612    17  52757.225    52757.257    52890.674
138  TIM2+F+R3     26361.609    19  52761.218    52761.259    52910.367
146  TIM2+F+I+R2   26361.637    18  52759.273    52759.309    52900.572
155  TIM2e         26703.027    12  53430.055    53430.071    53524.254
156  TIM2e+I       26703.026    13  53432.052    53432.072    53534.101
157  TIM2e+G4      26703.011    13  53432.021    53432.040    53534.070
158  TIM2e+I+G4    26703.041    14  53434.082    53434.105    53543.981
159  TIM2e+R2      26702.996    14  53433.993    53434.015    53543.892
160  TIM2e+R3      26702.990    16  53437.980    53438.009    53563.579
168  TIM2e+I+R2    26703.021    15  53436.041    53436.066    53553.790
177  TIM+F         26361.418    15  52752.835    52752.861    52870.584
178  TIM+F+I       26361.407    16  52754.814    52754.843    52880.413
179  TIM+F+G4      26361.406    16  52754.812    52754.841    52880.411
180  TIM+F+I+G4    26361.436    17  52756.872    52756.905    52890.321
181  TIM+F+R2      26361.405    17  52756.810    52756.843    52890.259
182  TIM+F+R3      26361.405    19  52760.810    52760.850    52909.958
190  TIM+F+I+R2    26361.435    18  52758.871    52758.907    52900.169
199  TIMe          26703.033    12  53430.065    53430.082    53524.264
200  TIMe+I        26703.032    13  53432.063    53432.083    53534.113
201  TIMe+G4       26703.031    13  53432.062    53432.081    53534.111
202  TIMe+I+G4     26703.066    14  53434.132    53434.154    53544.031
203  TIMe+R2       26703.030    14  53434.060    53434.082    53543.959
204  TIMe+R3       26703.030    16  53438.059    53438.088    53563.658
212  TIMe+I+R2     26703.064    15  53436.129    53436.154    53553.878
221  TPM3u+F       26363.681    14  52755.362    52755.384    52865.261
222  TPM3u+F+I     26363.678    15  52757.355    52757.381    52875.104
223  TPM3u+F+G4    26363.675    15  52757.350    52757.375    52875.099
224  TPM3u+F+I+G4  26363.700    16  52759.400    52759.428    52884.998
225  TPM3u+F+R2    26363.668    16  52759.336    52759.365    52884.935
226  TPM3u+F+R3    26363.666    18  52763.332    52763.368    52904.631
234  TPM3u+F+I+R2  26363.693    17  52761.385    52761.418    52894.834
243  TPM3          26705.424    11  53432.848    53432.862    53519.197
244  TPM3+I        26705.424    12  53434.848    53434.865    53529.047
245  TPM3+G4       26705.424    12  53434.848    53434.865    53529.047
246  TPM3+I+G4     26705.455    13  53436.910    53436.930    53538.959
247  TPM3+R2       26705.424    13  53436.848    53436.867    53538.897
248  TPM3+R3       26705.424    15  53440.848    53440.873    53558.597
256  TPM3+I+R2     26705.455    14  53438.910    53438.932    53548.809
265  TPM2u+F       26363.676    14  52755.352    52755.374    52865.251
266  TPM2u+F+I     26363.668    15  52757.336    52757.362    52875.085
267  TPM2u+F+G4    26363.659    15  52757.317    52757.343    52875.066
268  TPM2u+F+I+G4  26363.682    16  52759.364    52759.392    52884.963
269  TPM2u+F+R2    26363.646    16  52759.293    52759.322    52884.892
270  TPM2u+F+R3    26363.640    18  52763.279    52763.315    52904.578
278  TPM2u+F+I+R2  26363.661    17  52761.322    52761.354    52894.771
287  TPM2          26705.192    11  53432.384    53432.398    53518.733
288  TPM2+I        26705.186    12  53434.373    53434.389    53528.572
289  TPM2+G4       26705.168    12  53434.336    53434.353    53528.535
290  TPM2+I+G4     26705.191    13  53436.382    53436.401    53538.431
291  TPM2+R2       26705.149    13  53436.297    53436.317    53538.346
292  TPM2+R3       26705.140    15  53440.281    53440.306    53558.030
300  TPM2+I+R2     26705.165    14  53438.330    53438.352    53548.229
309  K3Pu+F        26363.483    14  52754.967    52754.989    52864.866
310  K3Pu+F+I      26363.472    15  52756.945    52756.970    52874.694
311  K3Pu+F+G4     26363.471    15  52756.942    52756.967    52874.691
312  K3Pu+F+I+G4   26363.496    16  52758.992    52759.021    52884.591
313  K3Pu+F+R2     26363.467    16  52758.934    52758.963    52884.533
314  K3Pu+F+R3     26363.466    18  52762.932    52762.968    52904.231
322  K3Pu+F+I+R2   26363.493    17  52760.987    52761.019    52894.436
331  K3P           26705.252    11  53432.505    53432.519    53518.854
332  K3P+I         26705.251    12  53434.503    53434.519    53528.702
333  K3P+G4        26705.251    12  53434.501    53434.518    53528.700
334  K3P+I+G4      26705.279    13  53436.559    53436.578    53538.608
335  K3P+R2        26705.246    13  53436.493    53436.512    53538.542
336  K3P+R3        26705.246    15  53440.492    53440.517    53558.241
344  K3P+I+R2      26705.276    14  53438.553    53438.575    53548.452
353  TN+F          26361.656    14  52751.312    52751.334    52861.211
354  TN+F+I        26361.654    15  52753.308    52753.333    52871.057
355  TN+F+G4       26361.653    15  52753.307    52753.332    52871.056
356  TN+F+I+G4     26361.684    16  52755.367    52755.396    52880.966
357  TN+F+R2       26361.653    16  52755.306    52755.335    52880.905
358  TN+F+R3       26361.653    18  52759.306    52759.342    52900.605
366  TN+F+I+R2     26361.683    17  52757.367    52757.399    52890.816
375  TNe           26703.227    11  53428.455    53428.469    53514.804
376  TNe+I         26703.226    12  53430.453    53430.469    53524.652
377  TNe+G4        26703.226    12  53430.452    53430.468    53524.651
378  TNe+I+G4      26703.261    13  53432.522    53432.541    53534.571
379  TNe+R2        26703.225    13  53432.451    53432.470    53534.500
380  TNe+R3        26703.225    15  53436.450    53436.476    53554.199
388  TNe+I+R2      26703.260    14  53434.521    53434.543    53544.420
397  HKY+F         26363.710    13  52753.421    52753.440    52855.470
398  HKY+F+I       26363.710    14  52755.420    52755.442    52865.319
399  HKY+F+G4      26363.709    14  52755.419    52755.441    52865.318
400  HKY+F+I+G4    26363.737    15  52757.475    52757.500    52875.224
401  HKY+F+R2      26363.709    15  52757.418    52757.443    52875.167
402  HKY+F+R3      26363.709    17  52761.418    52761.450    52894.866
410  HKY+F+I+R2    26363.737    16  52759.474    52759.502    52885.073
419  K2P           26705.440    10  53430.881    53430.892    53509.380
420  K2P+I         26705.440    11  53432.880    53432.894    53519.229
421  K2P+G4        26705.440    11  53432.879    53432.893    53519.228
422  K2P+I+G4      26705.470    12  53434.941    53434.957    53529.140
423  K2P+R2        26705.439    12  53434.878    53434.895    53529.078
424  K2P+R3        26705.439    14  53438.878    53438.900    53548.777
432  K2P+I+R2      26705.470    13  53436.940    53436.959    53538.989
441  F81+F         26385.670    12  52795.340    52795.357    52889.539
442  F81+F+I       26385.670    13  52797.340    52797.359    52899.389
443  F81+F+G4      26385.670    13  52797.340    52797.360    52899.389
444  F81+F+I+G4    26385.701    14  52799.403    52799.425    52909.302
445  F81+F+R2      26385.670    14  52799.340    52799.362    52909.239
446  F81+F+R3      26385.670    16  52803.340    52803.369    52928.939
454  F81+F+I+R2    26385.701    15  52801.403    52801.428    52919.152
463  JC            26726.679    9   53471.358    53471.367    53542.007
464  JC+I          26726.679    10  53473.358    53473.369    53551.857
465  JC+G4         26726.679    10  53473.358    53473.369    53551.857
466  JC+I+G4       26726.712    11  53475.423    53475.437    53561.772
467  JC+R2         26726.679    11  53475.358    53475.372    53561.707
468  JC+R3         26726.679    13  53479.358    53479.377    53581.407
476  JC+I+R2       26726.712    12  53477.423    53477.440    53571.622
Akaike Information Criterion:           TN+F
Corrected Akaike Information Criterion: TN+F
Bayesian Information Criterion:         HKY+F
Best-fit model: TN+F chosen according to AIC

All model information printed to PREF.model.gz
CPU time for ModelFinder: 0.126 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.142 seconds (0h:0m:0s)

NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -26385.670
2. Current log-likelihood: -26362.479
Optimal log-likelihood: -26362.448
Rate parameters:  A-C: 1.00000  A-G: 16.66170  A-T: 1.00000  C-G: 1.00000  C-T: 8.04541  G-T: 1.00000
Base frequencies:  A: 0.318  C: 0.214  G: 0.198  T: 0.269
Parameters optimization took 2 rounds (0.001 sec)
Wrote distance file to... 
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.000159278 secs using 82.25% CPU
Computing ML distances took 0.000246 sec (of wall-clock time) 0.000173 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 2.9334e-05 secs using 95.45% CPU
Computing RapidNJ tree took 0.000092 sec (of wall-clock time) 0.000092 sec (of CPU time)
Log-likelihood of RapidNJ tree: -26362.536
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 99 parsimony trees... 0.022 second
Computing log-likelihood of 6 initial trees ... 0.001 seconds
Current best score: -26362.448

Do NNI search on 7 best initial trees
UPDATE BEST LOG-LIKELIHOOD: -26362.448
Finish initializing candidate tree set (7)
Current best tree score: -26362.448 / CPU time: 0.027
Number of iterations: 7
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
UPDATE BEST LOG-LIKELIHOOD: -26362.448
UPDATE BEST LOG-LIKELIHOOD: -26362.448
Iteration 10 / LogL: -26362.475 / Time: 0h:0m:0s
UPDATE BEST LOG-LIKELIHOOD: -26362.448
UPDATE BEST LOG-LIKELIHOOD: -26362.448
Iteration 20 / LogL: -26362.448 / Time: 0h:0m:0s
Iteration 30 / LogL: -26362.477 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 40 / LogL: -26362.469 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 50 / LogL: -26362.474 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 60 / LogL: -26362.474 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 70 / LogL: -26362.448 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 80 / LogL: -26362.448 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 90 / LogL: -26362.448 / Time: 0h:0m:0s (0h:0m:0s left)
Iteration 100 / LogL: -26362.448 / Time: 0h:0m:0s (0h:0m:0s left)
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:0s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -26362.448
2. Current log-likelihood: -26362.418
3. Current log-likelihood: -26362.389
4. Current log-likelihood: -26362.360
5. Current log-likelihood: -26362.332
6. Current log-likelihood: -26362.304
7. Current log-likelihood: -26362.276
8. Current log-likelihood: -26362.249
9. Current log-likelihood: -26362.223
10. Current log-likelihood: -26362.198
11. Current log-likelihood: -26362.173
12. Current log-likelihood: -26362.148
13. Current log-likelihood: -26362.124
14. Current log-likelihood: -26362.101
15. Current log-likelihood: -26362.079
16. Current log-likelihood: -26362.057
17. Current log-likelihood: -26362.036
18. Current log-likelihood: -26362.015
19. Current log-likelihood: -26361.995
20. Current log-likelihood: -26361.976
21. Current log-likelihood: -26361.957
22. Current log-likelihood: -26361.940
23. Current log-likelihood: -26361.923
24. Current log-likelihood: -26361.906
25. Current log-likelihood: -26361.890
26. Current log-likelihood: -26361.875
27. Current log-likelihood: -26361.861
28. Current log-likelihood: -26361.847
29. Current log-likelihood: -26361.834
30. Current log-likelihood: -26361.822
31. Current log-likelihood: -26361.810
32. Current log-likelihood: -26361.799
33. Current log-likelihood: -26361.788
Optimal log-likelihood: -26361.778
Rate parameters:  A-C: 1.00000  A-G: 12.41206  A-T: 1.00000  C-G: 1.00000  C-T: 6.12357  G-T: 1.00000
Base frequencies:  A: 0.318  C: 0.214  G: 0.198  T: 0.269
Parameters optimization took 33 rounds (0.007 sec)
BEST SCORE FOUND : -26361.778
Total tree length: 0.003

Total number of iterations: 101
CPU time used for tree search: 0.099 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.115 sec (0h:0m:0s)
Total CPU time used: 0.239 sec (0h:0m:0s)
Total wall-clock time used: 0.275 sec (0h:0m:0s)

Analysis results written to: 
  IQ-TREE report:                PREF.iqtree
  Maximum-likelihood tree:       PREF.treefile
  Likelihood distances:          PREF.mldist
  Screen log file:               PREF.log

Date and Time: Thu Feb 12 11:26:46 2026

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
bootstrap_parameters	`{"nonparametric_bootstrap": {"bcon": null, "bonly": null, "boot": null, "jack": null, "jack_prop": null, "tbe": false}, "ultrafast_bootstrap": {"bcor": "0.99", "beps": "0.5", "bnni": false, "boot_trees": false, "jack_prop": null, "nmax": "1000", "nstep": "100", "sampling": null, "ufboot": null, "ufjack": null, "wbtl": false}}`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
general_options	`{"epsilon": null, "keep_ident": false, "o": null, "s": {"values": [{"id": 118, "src": "hda"}]}, "safe": false, "seed": null, "seqtype": "DNA", "short_alignments": false, "t": null}`
likelihood_mapping	`{"lmap": null, "lmclust": null, "quartetlh": false}`
miscellaneous_options	`{"blmax": null, "blmin": null, "fconst": null}`
modelling_parameters	{"automatic_model": {"cmax": "10", "cmin": "2", "cond_model": {"__current_case__": 0, "m": null, "opt_custommodel": "true"}, "madd": null, "mdef": null, "merge_strategy": {"__current_case__": 0, "merge": "none"}, "merit": "AIC", "mfreq": null, "modelomatic": false, "mrate": null, "mset": null, "msub": "nuclear", "mtree": false}, "partition_model": {"model_selection": {"__current_case__": 0, "model": "none"}}, "rate_heterogeneity": {"alpha_min": null, "gamma_median": false, "i": null, "mlrate": false, "opt_gamma_inv": false, "rate": false}, "site_specific_frequency": {"freq_max": false, "site_freq": null, "tree_freq": null}, "specifying_substitution": {"mix_opt": false}}
time_tree	`{"clock_sd": null, "date_ci": null, "date_no_outgroup": false, "date_options": null, "date_outlier": null, "date_root": null, "date_source": {"__current_case__": 0, "select_source": "none"}, "date_tip": null}`
tree_parameters	{"ancestral_state": {"ancestral": false, "asr_min": null}, "computing_robinson_foulds": {"tree_dist": null, "tree_dist2": null, "tree_dist_all": false}, "concordance_factor": {"cf_quartet": false, "cf_verbose": false, "df_tree": false, "gcf": null, "scf": null}, "constructing_consensus": {"burnin": null, "connet": false, "contree": false, "sup_min": "0.0", "support": null, "suptag": null}, "generating_random": {"branch_max": null, "branch_mean": null, "branch_min": null, "r": null, "rand": null}, "single_branch": {"abayes": false, "alrt": null, "lbp": null}, "symmetry_test": {"symtest": false, "symtest_keep_zero": false, "symtest_pval": null, "symtest_remove_bad": false, "symtest_remove_good": false, "symtest_type": null}, "tree_search": {"allnni": false, "fast": false, "g": null, "n": null, "nbest": "5", "ninit": "100", "nstop": "100", "ntop": "20", "perturb": "0.5", "polytomy": false, "radius": "6", "show_lh": false, "terrace": false, "tree_fix": false, "treels": false}, "tree_topology": {"test": null, "test_au": false, "test_weight": false, "trees": null}}

Step 40: convert to nex (toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-d7b6982b52f20b35fcbe3a2dcac917d683d5f7d9:141d853a536dd1614dcc5311f82f5dc0eb17e776-1

Command Line:

seqret -sequence '/tmp/tmpfplbed14/files/8/1/a/dataset_81a9849e-3521-468c-ba06-ad39e0c7af18.dat' -outseq '/tmp/tmpfplbed14/job_working_directory/000/58/outputs/dataset_537afa24-d930-4918-b8f7-d3203f5c0a26.dat' -feature no -firstonly no -osformat2 nexus -auto

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
feature	`"no"`
firstonly	`"no"`
out_format1	`"nexus"`

Step 41: MrBayes (toolshed.g2.bx.psu.edu/repos/nml/mrbayes/mrbayes/1.0.2):

step_state: scheduled

Jobs

Job 1:

Job state is error

Container:

```
quay.io/biocontainers/mrbayes:3.2.6--0
```

Command Line:

mb /tmp/tmpfplbed14/job_working_directory/000/60/configs/tmp4dk_anrn > /tmp/tmpfplbed14/job_working_directory/000/60/outputs/dataset_d1f04e8c-b1fb-48c2-a048-ba26920ca97b.dat

Exit Code:

```
1
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"nexus"`
__workflow_invocation_uuid__	`"fce87a9407e811f189517c1e52058f08"`
append	`false`
burninfrac	`"0.25"`
checkfreq	`"100000"`
chromInfo	`"/tmp/tmpfplbed14/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`""`
model	`"lset nst=6"`
nchain	`"4"`
ngen	`"5000000"`
nrun	`"2"`
outgroup	`"1"`
plot	`true`
printfreq	`"1000"`
rates	`"equal"`
samplefreq	`"1000"`
seed	`"5"`
stoprule	`"no"`
sump	`true`
sumt	`true`
swapseed	`"5"`

Other invocation details
- history_id
  - cacf01959bb7d434
- history_state
  - error
- invocation_id
  - cacf01959bb7d434
- invocation_state
  - scheduled
- workflow_id
  - 6b7ea9126a89e630

mvdbeek · 2026-02-13T14:32:22Z

Step 41: MrBayes (toolshed.g2.bx.psu.edu/repos/nml/mrbayes/mrbayes/1.0.2) failed. I'm afraid there's nothing in the stderr that would tell us what went wrong.

initial commit of the workflow to the fork!

35ba161

Smkingsize added 2 commits February 11, 2026 11:02

wrote new tests for outputs further down the workflow and if they suc…

7b5d209

…ceeded this indicates other tools ran also correctly!

"release": "0,1" was positioned correctly withen the .ga file

114bb49

Smkingsize marked this pull request as ready for review February 11, 2026 12:12

updated databases to be selected by the user and choose databases tha…

829a8cd

…t are available on al servers for testing!

loaded test file from zenodo!

ce08fd0

updated test!

65c2d38

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

add "VirDetectorGalaxy" workflow for virial analysis from nanopore data.#1102

add "VirDetectorGalaxy" workflow for virial analysis from nanopore data.#1102
Smkingsize wants to merge 6 commits intogalaxyproject:mainfrom
Smkingsize:main

Smkingsize commented Feb 11, 2026 •

edited

Loading

Uh oh!

github-actions bot commented Feb 11, 2026

Uh oh!

github-actions bot commented Feb 11, 2026

Uh oh!

github-actions bot commented Feb 11, 2026

Uh oh!

Smkingsize commented Feb 11, 2026 •

edited

Loading

Uh oh!

mvdbeek commented Feb 11, 2026

Uh oh!

github-actions bot commented Feb 11, 2026

Uh oh!

github-actions bot commented Feb 12, 2026

Workflow invocation details

Uh oh!

mvdbeek commented Feb 13, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

Smkingsize commented Feb 11, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

github-actions bot commented Feb 11, 2026

Test Results (powered by Planemo)

Test Summary

Uh oh!

github-actions bot commented Feb 11, 2026

Test Results (powered by Planemo)

Test Summary

Uh oh!

github-actions bot commented Feb 11, 2026

Test Results (powered by Planemo)

Test Summary

Uh oh!

Smkingsize commented Feb 11, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

mvdbeek commented Feb 11, 2026

Uh oh!

github-actions bot commented Feb 11, 2026

Test Results (powered by Planemo)

Test Summary

Uh oh!

github-actions bot commented Feb 12, 2026

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Uh oh!

mvdbeek commented Feb 13, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Smkingsize commented Feb 11, 2026 •

edited

Loading

Smkingsize commented Feb 11, 2026 •

edited

Loading