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AI-generated troubleshooting analysis is available in the AI Analysis tab.
Resume
To resume this run, resubmit with same or fixed code. You can also change other parameters but that will affect caching behavior.
-resume a69d1aac-8670-4e19-b97f-2a6fb56f9b99 -name sarek-low-input-study-tools-20260529-035022
Error Report
Error executing process > 'NFCORE_SAREK:SAREK:CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT (1029_5PA-T1-TDNA-1_A23NN2MLT4_1)'
Caused by:
Process `NFCORE_SAREK:SAREK:CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT (1029_5PA-T1-TDNA-1_A23NN2MLT4_1)` terminated with an error exit status (1)
Command executed:
bai_mapped_count.py 1029_5PA-T1-TDNA-1_A23NN2MLT4_1.recalibrated.bam.bai > 1029_5PA-T1-TDNA-1_A23NN2MLT4_1.mapped_count.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT":
python: $(python3 --version | sed 's/Python //')
bai_mapped_count: 1.0.0
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Work dir:
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/b4602b79f270beb1e69e9a72445da6
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/multiqc:1.25.1--pyhdfd78af_0
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Workflow
- Language / Cluster
- Nextflow / pltf-dev
- Session ID
- a69d1aac-8670-4e19-b97f-2a6fb56f9b99
- Work Dir
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work
- Submitted By
- sgreer
- Resumed
- No
Cost and Runtime
- Status
- failed
- Cost
- $1.02
- Outputs
- 9 MB
- Started
- May 28, 2026 8:51 PM
- Completed
- May 28, 2026 8:55 PM
- Duration
- 4m 29s
- Post-workflow Transfer
- 3s
- Exit Status
- 1
- Peak Tasks / CPU / Mem
- 5 / 5 / 12.0 GB