Process single_sample_wgs:run_HaplotypeCallerGVCF_GATK (30) terminated with an error exit status (1)

[raagagrawal]

Describe the issue

Pipeline fails at HaplotypeCallerGVCF

Error executing process > 'single_sample_wgs:run_HaplotypeCallerGVCF_GATK (30)'

Caused by:
  Process `single_sample_wgs:run_HaplotypeCallerGVCF_GATK (30)` terminated with an error exit status (1)

Command executed:

  set -euo pipefail
  
  gatk --java-options "-Xmx7168m -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Djava.io.tmpdir=/scratch"         HaplotypeCaller         --input LAPRCOLB000001-N001-C01-U-normal_recalibrated_0000.bam         --output LAPRCOLB000001-N001-C01-U_0000_raw_variants.g.vcf.gz         --reference Homo_sapiens_assembly38.fasta         --verbosity INFO         --output-mode EMIT_VARIANTS_ONLY         --emit-ref-confidence GVCF         --dbsnp resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz         --sample-ploidy 2         --intervals 0000-scattered.interval_list

Command exit status:
  1

Command output:
  (empty)

• Pipeline release version: 9.1.0
• Cluster you are using (SGE/Slurm-Dev/Slurm-Test): Slurm-Dev
• Node type (F2s (lowmem) / F72s (midmem) / M64s (execute)): F72
• Submission method (interactive/submission script): Script
• Actual submission script (python submission script, "nextflow run ...", etc.): python submission script
• Sbatch or qsub command and logs if applicable: sbatch
• Config files: /hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/call-gsnp/config/template.config
• Path to the working directory: /hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/call-gsnp/config
• Any logs produced by the pipeline: /hot/user/ragrawal/Liss-Agrawal-PRAD-COLB/call-gsnp/config/call-gsnp.log

To Reproduce

1. ./submit.sh
2. Errors out

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
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Additional context
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[yashpatel6]

The issue is arising from the tumour_id field in the input CSV not matching the actual SM tag in the BAM header. You'll want to make sure these two match. The SM tag can be found with samtools view -H:

@RG	ID:379.L004-02.SeqL004-02	CN:UNGC	LB:BCLB1	PL:ILLUMINA	PU:HV5W3DSX3.L004-02.BCLB1_S99	SM:BCLB1_S99
@RG	ID:395.L003.SeqL003	CN:UNGC	LB:BCLB1	PL:ILLUMINA	PU:HWLLGDSX3.L003.BCLB1_S3	SM:BCLB1_S3
@RG	ID:395.L004-01.SeqL004-01	CN:UNGC	LB:BCLB1	PL:ILLUMINA	PU:HWLLGDSX3.L004-01.BCLB1_S3	SM:BCLB1_S3

[raagagrawal]

If I have multiple SM tags under a single sample ID - I should then make multiple input csvs for each SM then right?

Thank you for helping me find where to get the SM tags!