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Resume
To resume this run, resubmit with same or fixed code. You can also change other parameters but that will affect caching behavior.
-resume s3files-daq-69f0bb1a
Error Report
Error executing process > 'DAQ:SENTIEON_BWAMEM (Sig_18_tissue;L001;0001)'
Caused by:
Process `DAQ:SENTIEON_BWAMEM (Sig_18_tissue;L001;0001)` terminated with an error exit status (1)
Command executed:
INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`
export bwt_max_mem=112G
sentieon bwa mem \
-K 100000000 -Y -R '@RG\tID:REGRESSION.Sig_18_tissue.L001\tPU:L001\tSM:Sig_18_tissue\tLB:Sig_18_tissue\tDS:s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA' \
-t 31 \
$INDEX \
Sig_18_tissue_R1.fastq.gz Sig_18_tissue_R2.fastq.gz \
| sentieon util sort \
-r Homo_sapiens_assembly38.fasta \
-t 31 \
-o Sig_18_tissue.bam \
--sam2bam \
-
# When outputting CRAM, sentieon util sort may create a spurious .bai index.
# Remove it since CRAM uses .crai indices.
if [ "bam" = "cram" ] && [ -f "Sig_18_tissue.cram.bai" ]; then
rm -f Sig_18_tissue.cram.bai
fi
cat <<-END_VERSIONS > versions.yml
"DAQ:SENTIEON_BWAMEM":
sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Failed to open sentieon license file : No such file or directory
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o Sig_18_tissue.bam --sam2bam -
Failed to open sentieon license file : No such file or directory
Work dir:
s3://natera-rnd-pltf-stage-nextflow-scratch-01/work/83/dfcbb5a8e742317f131d9540135404
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/markduplicates_sentieon:202308.03-1
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Workflow
- Language / Cluster
- Nextflow / pltf-dev
- Session ID
- 89d15aac-0e76-4526-8530-6cd2cd6708cb
- Source
- /code/main.nf
- Work Dir
- s3://natera-rnd-pltf-stage-nextflow-scratch-01/work
- Submitted By
- -
- Resumed
- No
Cost and Runtime
- Status
- failed
- Outputs
- computing…
- Started
- Apr 28, 2026 6:51 AM
- Completed
- Apr 28, 2026 7:13 AM
- Duration
- 21m 31s
- Post-workflow Transfer
- 3s
- Exit Status
- 1
- Peak Tasks / CPU / Mem
- 39 / 993 / 3.9 TB