se-wgs-variation: convert asserts to list form (blocked by bcftools concat SIGSEGV) by jmchilton · Pull Request #1277 · galaxyproject/iwc

jmchilton · 2026-07-10T21:09:21Z

Opened by Claude (AI assistant) on behalf of @jmchilton — not authored by them personally.

Summary

Convert the se-wgs-variation asserts: blocks from duplicate-keyed dict form to list form so every assertion runs (same fix as the passing-subset PR). Split out on its own because the test currently errors for a reason unrelated to this change, and I didn't want it dragging the green set red.

Why this is red (not our change)

IWC CI only tests changed workflows, so editing this test file is what caused se-wgs-variation to run at all — surfacing a pre-existing crash:

CRITICAL: command failed with return code -11:
bcftools concat -a -O z -o concat.vcf.gz 0.vcf.gz 1.vcf.gz 2.vcf.gz

rc -11 = SIGSEGV. bcftools concat segfaults inside lofreq_call's biocontainer while combining the (empty — "0 tests performed", "idxstats reports no reads mapped") VCF chunks. That's a Galaxy job-level crash, upstream of anything the test YAML does — the assertion conversion cannot cause it. The workflow errors before assertions are ever evaluated, so this change can't be green-validated until the crash is resolved.

Tracking

Determine whether the bcftools concat SIGSEGV is biocontainer/version-specific or a broader environment regression (it may affect other bcftools/lofreq workflows — only changed ones get tested, so it's under-reported)
Once the crash is fixed, confirm this workflow's assertions pass and fold this in

Do not merge while red — this PR is a holding place for the assertion fix + a paper trail on the crash.

YAML collapses duplicate mapping keys (last wins), so repeated has_text entries only ran the last assertion per type. Convert to list form so each runs. Isolated from the passing-subset PR: this workflow's test currently ERRORS for a reason unrelated to this change — bcftools concat segfaults (SIGSEGV, rc -11) inside lofreq_call's biocontainer while combining empty VCF chunks. IWC only tests changed workflows, so touching this file is what surfaced the pre-existing crash. Kept separate so it doesn't block the genuinely-green set. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

github-actions · 2026-07-10T21:33:12Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ se-wgs-variation.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Single End Collection:
- step_state: scheduled
Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2:
- step_state: scheduled

Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/fastp:0.24.0--heae3180_1

Command Line:

ln -sf '/tmp/tmpah5_7nod/files/7/a/1/dataset_7a18386d-f9d9-414b-b44d-17039d119d56.dat' 'SRR11605118.fastqsanger' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11605118.fastqsanger'  -i 'SRR11605118.fastqsanger'   -o first.fastqsanger                                               && mv first.fastqsanger '/tmp/tmpah5_7nod/job_working_directory/000/3/outputs/dataset_ef7e4cfe-8908-4fd6-8403-a719f3d6d97c.dat'

Exit Code:

```
0
```

Standard Error:

Detecting adapter sequence for read1...
No adapter detected for read1

Read1 before filtering:
total reads: 0
total bases: 0
Q20 bases: 0(-nan%)
Q30 bases: 0(-nan%)

Read1 after filtering:
total reads: 0
total bases: 0
Q20 bases: 0(-nan%)
Q30 bases: 0(-nan%)

Filtering result:
reads passed filter: 0
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 0
bases trimmed due to adapters: 0

Duplication rate (may be overestimated since this is SE data): 0%

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for SRR11605118.fastqsanger -i SRR11605118.fastqsanger -o first.fastqsanger 
fastp v0.24.0, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 0, "adapter_trimming_options": {"adapter_sequence1": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_tail1": null}, "in1": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "single"}`

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-c742dccc9d8fabfcff2af0d8d6799dbc711366cf:a2e4688a25bd1726a756713d5233a63a5ac7f597-0

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpah5_7nod/files/1/b/1/dataset_1b16f350-5066-44b8-90b2-23519c7cf2be.dat' genome && ln -s -f '/tmp/tmpah5_7nod/files/1/b/1/dataset_1b16f350-5066-44b8-90b2-23519c7cf2be.dat' genome.fa &&   ln -f -s '/tmp/tmpah5_7nod/files/e/f/7/dataset_ef7e4cfe-8908-4fd6-8403-a719f3d6d97c.dat' input_f.fastq &&   THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -U 'input_f.fastq'                         --rg-id "SRR11605118"             --very-sensitive   2> >(tee '/tmp/tmpah5_7nod/job_working_directory/000/4/outputs/dataset_113d5917-62d3-49c6-a4ee-3e6578771a7a.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpah5_7nod/job_working_directory/000/4/outputs/dataset_84397c8d-1b84-4387-b47f-974fcec7a3e7.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
Unable to read file magic number
is_zstd_file: unable to read magic number
0 reads
0.00% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmpah5_7nod/files/1/b/1/dataset_1b16f350-5066-44b8-90b2-23519c7cf2be.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 7475
Using parameters --bmax 5607 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 5607 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3737 (target: 5606)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (5607) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 4574 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 4575 for bucket 1
Getting block 2 of 8
  Reserving size (5607) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 2668 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 2669 for bucket 2
Getting block 3 of 8
  Reserving size (5607) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 3483 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 3484 for bucket 3
Getting block 4 of 8
  Reserving size (5607) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 4420 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 4421 for bucket 4
Getting block 5 of 8
  Reserving size (5607) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 4901 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 4902 for bucket 5
Getting block 6 of 8
  Reserving size (5607) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 3813 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 3814 for bucket 6
Getting block 7 of 8
  Reserving size (5607) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 2667 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 2668 for bucket 7
Getting block 8 of 8
  Reserving size (5607) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 3370 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 3371 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 8954
fchr[G]: 14446
fchr[T]: 20309
fchr[$]: 29903
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4204461 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 7480 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 29903
    bwtLen: 29904
    sz: 7476
    bwtSz: 7476
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1869
    offsSz: 7476
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 156
    numLines: 156
    ebwtTotLen: 9984
    ebwtTotSz: 9984
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 7475
Using parameters --bmax 5607 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 5607 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 3737 (target: 5606)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (5607) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 2598 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 2599 for bucket 1
Getting block 2 of 8
  Reserving size (5607) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 5142 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 5143 for bucket 2
Getting block 3 of 8
  Reserving size (5607) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 4371 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 4372 for bucket 3
Getting block 4 of 8
  Reserving size (5607) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 4433 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 4434 for bucket 4
Getting block 5 of 8
  Reserving size (5607) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 3267 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 3268 for bucket 5
Getting block 6 of 8
  Reserving size (5607) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 2880 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 2881 for bucket 6
Getting block 7 of 8
  Reserving size (5607) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 5175 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 5176 for bucket 7
Getting block 8 of 8
  Reserving size (5607) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 2030 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 2031 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 8954
fchr[G]: 14446
fchr[T]: 20309
fchr[$]: 29903
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4204461 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 7480 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 29903
    bwtLen: 29904
    sz: 7476
    bwtSz: 7476
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 1869
    offsSz: 7476
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 156
    numLines: 156
    ebwtTotLen: 9984
    ebwtTotSz: 9984
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "--very-sensitive"}`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 0, "aligned_file": false, "input_1": {"values": [{"id": 2, "src": "dce"}]}, "type": "single", "unaligned_file": false}`
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 1, "src": "hda"}]}, "source": "history"}`
rg	`{"__current_case__": 2, "rg_selector": "set_id_auto"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/picard:3.1.1--hdfd78af_0

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmpah5_7nod/files/8/4/3/dataset_84397c8d-1b84-4387-b47f-974fcec7a3e7.dat' 'SRR11605118' &&  picard MarkDuplicates  --INPUT 'SRR11605118' --OUTPUT '/tmp/tmpah5_7nod/job_working_directory/000/5/outputs/dataset_798d8dd8-c87b-4203-95c8-4cf5e55c981a.dat'  --METRICS_FILE '/tmp/tmpah5_7nod/job_working_directory/000/5/outputs/dataset_efbd4a7d-e172-4018-ac09-065821e5fdb6.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmpah5_7nod/job_working_directory/000/5/tmp
Jul 10, 2026 9:25:27 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmpah5_7nod/job_working_directory/000/5/working/SRR11605118, Error parsing SAM header. @RG line missing SM tag. Line:
@RG	ID:SRR11605118
Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmpah5_7nod/job_working_directory/000/5/working/SRR11605118, Error parsing SAM header. @RG line missing SM tag. Line:
@RG	ID:SRR11605118

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
inputFile	__identifier__
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/multiqc:1.27--pyhdfd78af_0

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&     ln -s '/tmp/tmpah5_7nod/files/1/8/1/dataset_1811a94e-6a21-40e4-b755-7b758135e7ae.dat' 'multiqc_WDir/fastp_0/SRR11605118fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR11605118fastp.json' || die "'report_title' or 'report_title' not found in the file" &&  mkdir multiqc_WDir/bowtie2_1 &&         grep -Pq '% overall alignment rate' /tmp/tmpah5_7nod/files/1/1/3/dataset_113d5917-62d3-49c6-a4ee-3e6578771a7a.dat || die "Module 'bowtie2: '% overall alignment rate' not found in the file 'SRR11605118'" && ln -s '/tmp/tmpah5_7nod/files/1/1/3/dataset_113d5917-62d3-49c6-a4ee-3e6578771a7a.dat' 'multiqc_WDir/bowtie2_1/SRR11605118'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -Pq 'MarkDuplicates' /tmp/tmpah5_7nod/files/e/f/b/dataset_efbd4a7d-e172-4018-ac09-065821e5fdb6.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR11605118'" && ln -s '/tmp/tmpah5_7nod/files/e/f/b/dataset_efbd4a7d-e172-4018-ac09-065821e5fdb6.dat' 'multiqc_WDir/picard_2/markdups_0/SRR11605118'  &&      multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.27

     version_check | MultiQC Version v1.35 now available!
       file_search | Search path: /tmp/tmpah5_7nod/job_working_directory/000/6/working/multiqc_WDir

    MarkDuplicates | Skipping MarkDuplicates sample 'SRR11605118' as log contained no reads
    MarkDuplicates | Skipping MarkDuplicates sample 'SRR11605118' as log contained no reads
    MarkDuplicates | Skipping MarkDuplicates sample 'SRR11605118' as log contained no reads
             fastp | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 180
-rw-r--r-- 1 1001 1001     95 Jul 10 21:26 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001    873 Jul 10 21:26 multiqc.log
-rw-r--r-- 1 1001 1001    121 Jul 10 21:26 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 128998 Jul 10 21:26 multiqc_data.json
-rw-r--r-- 1 1001 1001  25884 Jul 10 21:26 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001    200 Jul 10 21:26 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     26 Jul 10 21:26 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001    161 Jul 10 21:26 multiqc_sources.txt
-rw-r--r-- 1 1001 1001      0 Jul 10 21:26 picard_MarkIlluminaAdapters_histogram.txt
-rw-r--r-- 1 1001 1001      0 Jul 10 21:26 picard_MeanQualityByCycle_histogram.txt
-rw-r--r-- 1 1001 1001      0 Jul 10 21:26 picard_QualityScoreDistribution_histogram.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 6, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]`
saveLog	`"false"`
title	`""`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15

Command Line:

ln -s '/tmp/tmpah5_7nod/files/1/b/1/dataset_1b16f350-5066-44b8-90b2-23519c7cf2be.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmpah5_7nod/files/7/9/8/dataset_798d8dd8-c87b-4203-95c8-4cf5e55c981a.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpah5_7nod/job_working_directory/000/7/outputs/dataset_cb0044ae-dcea-46a2-82ce-784d13144575.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15

Command Line:

ln -s '/tmp/tmpah5_7nod/files/1/b/1/dataset_1b16f350-5066-44b8-90b2-23519c7cf2be.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpah5_7nod/files/c/b/0/dataset_cb0044ae-dcea-46a2-82ce-784d13144575.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is error

Container:

quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15

Command Line:

ln -s '/tmp/tmpah5_7nod/files/1/b/1/dataset_1b16f350-5066-44b8-90b2-23519c7cf2be.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmpah5_7nod/files/0/1/f/dataset_01f31fc9-948d-4589-9574-4bb82b156782.dat' reads.bam && ln -s -f '/tmp/tmpah5_7nod/files/_metadata_files/e/0/7/metadata_e07a31b9-5521-47be-b51f-96e72d6411af.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 5 --max-depth 1000000  --min-bq 30 --min-alt-bq 30    --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.0005 --bonf dynamic --no-default-filter  reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_custom

Exit Code:

```
1
```

Standard Error:

Executing lofreq filter -i /tmp/lofreq2-call-dyn-bonf.oAOqen -o /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/0.vcf.gz --no-defaults --snvqual-thresh 33 --indelqual-thresh 33
Number of substitution tests performed: 0
Number of indel tests performed: 0
Successful exit.
Executing lofreq filter -i /tmp/lofreq2-call-dyn-bonf.Svhz7e -o /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/1.vcf.gz --no-defaults --snvqual-thresh 33 --indelqual-thresh 33
Number of substitution tests performed: 0
Number of indel tests performed: 0
Successful exit.
Executing lofreq filter -i /tmp/lofreq2-call-dyn-bonf.b5LaEs -o /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/2.vcf.gz --no-defaults --snvqual-thresh 33 --indelqual-thresh 33
Number of substitution tests performed: 0
Number of indel tests performed: 0
Successful exit.

Standard Output:

INFO [2026-07-10 21:26:42,685]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam

WARNING [2026-07-10 21:26:42,690]: Looks like the index for reads.bam is a bit old (idxstats reports no reads mapped). Reindexing should solve this. Will continue by calling samtools, so no need to worry for now though.
INFO [2026-07-10 21:26:42,696]: Adding 3 commands to mp-pool
Checking the headers and starting positions of 3 files
CRITICAL [2026-07-10 21:26:43,060]: The following command failed with return code -11: bcftools concat -a -O z -o /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/concat.vcf.gz /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/0.vcf.gz /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/1.vcf.gz /tmp/tmpah5_7nod/job_working_directory/000/9/tmp/lofreq2_call_parallel1tqmrwu8/2.vcf.gz

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 11: SnpEff eff covid19 version (toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"a59f2cce7ca511f18d8470a8a51c800f"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpah5_7nod/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"]`
generate_stats	`true`
genome_version	`"NC_045512.2"`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - 9ec9631880fbf008
- history_state
  - error
- invocation_id
  - 9ec9631880fbf008
- invocation_state
  - scheduled
- workflow_id
  - 9ec9631880fbf008

jmchilton · 2026-07-13T20:43:43Z

Posted by Claude (AI assistant) on behalf of @jmchilton — not authored by them personally.

Root cause found + upstream fix filed

The red here is not the assert conversion — it's a pre-existing crash this workflow surfaces (IWC only tests changed workflows). Tracked it all the way down:

Chain: lofreq call-parallel splits the reference into regions, calls per region, and merges the per-region VCFs with bcftools concat -a (lofreq2_call_pparallel.py, concat_vcf_files). The SE test data leaves some regions with no reads / no called variants → header-only VCFs → bcftools concat -a segfaults (SIGSEGV, rc -11).

Why: it's a bcftools regression — samtools/bcftools#2286, "bcftools concat segfault if VCF files contain only headers." Present in 1.21, fixed in 1.22. The pinned lofreq_call/2.1.5 biocontainer bundles exactly bcftools 1.21, and lofreq calls bcftools from PATH, so it inherits the crash.

Verified in the shipped container (lofreq:2.1.5--py310h4966b78_15), same inputs/command:

bcftools	`concat -a` on header-only VCFs
1.20	✅ exit 0
1.21 (shipped)	❌ SIGSEGV (exit 139)
1.22	✅ exit 0

Fix filed upstream: bioconda-recipes PR bioconda/bioconda-recipes#67152 — pins bcftools >=1.22 in the lofreq recipe and bumps the build number. No lofreq code change needed.

Once that merges and the lofreq package rebuilds with bcftools ≥1.22, this workflow's bcftools concat should stop crashing and this PR's list-form conversion can be validated green. Keeping this PR parked until then.

jmchilton mentioned this pull request Jul 10, 2026

Convert duplicate-keyed asserts blocks to list form (passing subset) #1275

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se-wgs-variation: convert asserts to list form (blocked by bcftools concat SIGSEGV)#1277

se-wgs-variation: convert asserts to list form (blocked by bcftools concat SIGSEGV)#1277
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jmchilton:convert-asserts-se-wgs-variation

jmchilton commented Jul 10, 2026

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github-actions Bot commented Jul 10, 2026

Workflow invocation details

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jmchilton commented Jul 13, 2026

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jmchilton commented Jul 10, 2026

Summary

Why this is red (not our change)

Tracking

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github-actions Bot commented Jul 10, 2026

Test Results (powered by Planemo)

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Workflow invocation details

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jmchilton commented Jul 13, 2026

Root cause found + upstream fix filed

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