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-resume 0ed36893-044e-4e90-a120-215ba721f8f6 -name daq-altera-2890de2-b23fc2glt4
Error Report
Error executing process > 'DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1029_BG5-T1-TDNA-1_23FC2GLT4_s29)'
Caused by:
Process `DAQ:BAM_POSTDEDUP_QC:SEQTOOL (1029_BG5-T1-TDNA-1_23FC2GLT4_s29)` terminated with an error exit status (1)
Command executed:
# Matplotlib cache dir must be writable; default location may not be
export MPLCONFIGDIR=/tmp/matplotlib
all_qc \
-bam 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam \
-reference Homo_sapiens_assembly38.fasta \
-beds xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_footprint.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed \
-dbsnp_bed dbsnp138_hg38_common.bed \
-dbsnp_vcf dbsnp_146.hg38.vcf.gz \
-contamination_bed dbsnp_hg38_contam_sites.bed \
-output_folder 1029_BG5-T1-TDNA-1_23FC2GLT4_s29 \
-threads 31 \
merge_qc -folders 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/* -output 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29_full_basic_stats.tsv
head -n1 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29_full_basic_stats.tsv > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29_basic_stats.tsv
grep -e "$(basename xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed)" 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29_full_basic_stats.tsv >> 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29_basic_stats.tsv
cat <<-END_VERSIONS > versions.yml
"DAQ:BAM_POSTDEDUP_QC:SEQTOOL":
seqtool: 1.5.1
END_VERSIONS
Command exit status:
1
Command output:
mkdir -p 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/
cat xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed altera_v3_targets_postQC_hg38.bed altera_v3_targets_coding_postQC_hg38.bed altera_v3_targets_noncoding_postQC_hg38.bed xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_footprint.bed xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.bed FINAL_hotspot_list_07302025_hg38_sorted.bed | cut -f 1-3 | bedtools sort -g Homo_sapiens_assembly38.fasta.fai | bedtools merge > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/full_bed.bed
seqtool depth -bam 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam -bed 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/full_bed.bed -threads 6 | bgzip -c > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.depth.gz
saturation_plot -bams 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam -region chr20 -output 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/saturation_qc.tsv
fragment_size -bams 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam -region chr20 -output_prefix 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f Homo_sapiens_assembly38.fasta -l dbsnp_hg38_contam_sites.bed 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.mpileup && contamination -input 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.mpileup -dbsnp_vcf dbsnp_146.hg38.vcf.gz > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/contamination.tsv
seqtool noise -bam 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam -ref Homo_sapiens_assembly38.fasta -region chr20 -include_bed 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/full_bed.bed -exclude_bed dbsnp138_hg38_common.bed -threads 1 > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.noise_summary.tsv
tabix -s 1 -b 2 -e 2 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.depth.gz
seqtool depth_hist -nbins 500 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.depth.gz > 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.depth_hist.tsv
cat 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md -output 1029_BG5-T1-TDNA-1_23FC2GLT4_s29/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md/1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.depth.png
Command error:
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
[W::hts_idx_load3] The index file is older than the data file: 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 1029_BG5-T1-TDNA-1_23FC2GLT4_s29.md.bam.bai
103966it [00:00, 1039599.03it/s]
211246it [00:00, 1059087.55it/s]
320234it [00:00, 1073124.65it/s]
430305it [00:00, 1083989.57it/s]
543271it [00:00, 1100435.74it/s]
656597it [00:00, 1111572.53it/s]
768377it [00:00, 1113565.31it/s]
880873it [00:00, 1117173.48it/s]
992591it [00:00, 1111091.85it/s]
1104233it [00:01, 1112707.98it/s]
1194307it [00:01, 1103665.14it/s]
done loading BEDs.
[W::hts_idx_load3] The index file is older than the data file: dbsnp_146.hg38.vcf.gz.tbi
Traceback (most recent call last):
File "/opt/conda/bin/contamination", line 7, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/contamination.py", line 66, in main
gmaf = dbsnp_get_gmaf(dbsnp_records[0])
File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/contamination.py", line 27, in dbsnp_get_gmaf
fields = [re.sub("[\[\]]", "", af) for af in variant.info["CAF"]]
File "pysam/libcbcf.pyx", line 2608, in pysam.libcbcf.VariantRecordInfo.__getitem__
KeyError: 'Invalid INFO field: CAF'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/all_qc.py", line 74, in run_contamination
safe_system((
File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/all_qc.py", line 12, in safe_system
assert(os.system(cmd) == 0)
AssertionError
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/all_qc", line 7, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/seqtool_analysis/all_qc.py", line 264, in main
r.get()
File "/opt/conda/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
AssertionError
Work dir:
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/2e15f059c16cdacefe7083f50c29f5
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/seqtool:speedup-6873c4b
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Workflow
- Language / Cluster
- Nextflow / pltf-dev
- Session ID
- 0ed36893-044e-4e90-a120-215ba721f8f6
- Work Dir
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work
- Output Dir
- Deleted (1024.0 GB) by @abshah on 2026-05-29 6:10 PM. List of old outputs
- Submitted By
- abshah (project:altera)
- Resumed
- No
Cost and Runtime
- Status
- failed
- Cost
- $239.60
- Outputs
- Deleted
- Started
- Feb 12, 2026 10:44 AM
- Completed
- Feb 12, 2026 12:43 PM
- Duration
- 1h 59m
- Post-workflow Transfer
- 2s
- Exit Status
- 1
- Peak Tasks / CPU / Mem
- 373 / 7,521 / 29.8 TB