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To resume this run, resubmit with same or fixed code. You can also change other parameters but that will affect caching behavior.
-resume 6f7a9b55-45b8-4142-8120-ac93a2d73229 -name markdups-sentieon-test-2
Error Report
Error executing process > 'MARKDUPLICATES_SENTIEON (dna_s1343)'
Caused by:
Process `MARKDUPLICATES_SENTIEON (dna_s1343)` terminated with an error exit status (1)
Command executed:
sentieon driver -t 8 -i dna_s1343.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info dna_s1343.md.score
sentieon driver -t 8 -i dna_s1343.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info dna_s1343.md.score --metrics dna_s1343.md.metrics dna_s1343.md.bam
cat <<-END_VERSIONS > versions.yml
"MARKDUPLICATES_SENTIEON":
sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 8 -i dna_s1343.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info dna_s1343.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
Error: There is no readgroup (@RG) in BAM file dna_s1343.bam
Error: Invalid input BAM files
Work dir:
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/db90b145a8876d85b77253e55b84f3
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/markduplicates_sentieon:202308.03
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
- 6f7a9b55-45b8-4142-8120-ac93a2d73229
- Source
- /code/modules/local/markduplicates_sentieon/run.nf
- Work Dir
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work
- Submitted By
- abshah
- Resumed
- No
Cost and Runtime
- Status
- failed
- Cost
- $0.19
- Outputs
- 24 MB
- Started
- Jan 21, 2026 3:26 PM
- Completed
- Jan 21, 2026 3:35 PM
- Duration
- 8m 44s
- Post-workflow Transfer
- 9s
- Exit Status
- 1
- Peak Tasks / CPU / Mem
- 1 / 8 / 48.0 GB