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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 5ae7859b-4ddf-436e-a597-1f9b7643848f -name daq-markdups-test-2
Error Report
Error executing process > 'MARKDUPLICATES (dna_s1343)'
Caused by:
K8s pod image cannot be pulled -- rpc error: code = NotFound desc = failed to pull and unpack image "292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/markduplicates:4.5.0": failed to resolve image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/markduplicates:4.5.0: not found
Command executed:
gatk --java-options "-Xmx26214M -XX:-UsePerfData" \
MarkDuplicates \
--INPUT dna_s1343.bam \
--OUTPUT dna_s1343.md.bam \
--METRICS_FILE dna_s1343.md.metrics \
--TMP_DIR . \
--REFERENCE_SEQUENCE Homo_sapiens_assembly38.fasta \
-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
samtools index -@ 4 dna_s1343.md.bam
cat <<-END_VERSIONS > versions.yml
"MARKDUPLICATES":
gatk4: $(gatk --version 2>&1 | grep -E '^GATK' | sed 's/.*v//')
samtools: $(samtools --version | head -1 | sed 's/samtools //')
END_VERSIONS
Command exit status:
-
Command output:
(empty)
Work dir:
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/3754079349130516212eddec84f83a
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/markduplicates:4.5.0
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
- 5ae7859b-4ddf-436e-a597-1f9b7643848f
- Source
- /app/modules/local/markduplicates/run.nf
- Work Dir
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work
- Submitted By
- abshah
- Resumed
- No
Cost and Runtime
- Status
- failed
- Cost
- $0.00
- Outputs
- 3 MB
- Started
- Jan 16, 2026 4:17 PM
- Completed
- Jan 16, 2026 4:20 PM
- Duration
- 3m 1s
- Post-workflow Transfer
- 0s
- Exit Status
- -
- Peak Tasks / CPU / Mem
- 1 / 4 / 32.0 GB