Process multi_sample_wgs:recalibrate_base:run_ApplyBQSR_GATK (30) terminated with an error exit status (3)

[graceooh]

Describe the issue
Pipeline crashes for one of my samples
Says in log file:
Process multi_sample_wgs:recalibrate_base:run_ApplyBQSR_GATK (30) terminated with an error exit status (3)

• Pipeline release version- 9.1.0

• Cluster you are using (SGE/Slurm-Dev/Slurm-Test)

• Node type (F2s (lowmem) / F72s (midmem) / M64s (execute)) - F72

• Submission method (interactive/submission script) - submission script

• Actual submission script (python submission script, "nextflow run ...", etc.)

  python /hot/user/jieunoh/tools/tool-submit-nf/submit_nextflow_pipeline.py
  --nextflow_script /hot/software/pipeline/pipeline-call-gSNP/Nextflow/release/9.1.0/main.nf
  --sge_scheduler False
  --multi_node_mode False
  --nextflow_config "/hot/user/jieunoh/gap6_pilot/call-gSNP-input/2021-9127_bone/input_config_dir/BE-4.config"
  --pipeline_run_name BE-4-call-gsnp
  --partition_type F72
  --email [email protected]

• Sbatch or qsub command and logs if applicable

• Config files: /hot/user/jieunoh/gap6_pilot/call-gSNP-input/2021-9127_bone/input_config_dir/BE-4.config

• Path to the working directory

• Any logs produced by the pipeline:

/hot/user/jieunoh/gap6_pilot/call-gSNP-input/2021-9127_bone/log_files/BE-4-Bone/ BE-4-call-gsnp.log

To Reproduce
Steps to reproduce the behavior:

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4. See error

Expected behavior
Pipeline crashes possibly due to memory error

Screenshots

Additional context
Add any other context about the problem here.

[yashpatel6]

The issue seems to be disk space; the scratch space is running out. Could you try this run with a higher value for gatk_ir_compression? This controls the compression level of the output files produced by Indel Realignment; the default is 0 for fastest runtime but it also produced the least compressed outputs. Maybe try 5 since that's usually the current default GATK uses.

[graceooh]

Thank you! I'll let you know how it goes. :D