Error 137 in Epi2me TB-AMR Workflow

Question

[End]

Hello Biostars Community,

I am running a Nextflow pipeline, and it terminated with an error:

Error message:

Workflow execution completed unsuccessfully!  
The exit status of the task that caused the workflow execution to fail was: 137.  

Error executing process > 'pipeline:countReadsRegions (1)'  

Caused by:  
  Process `pipeline:countReadsRegions (1)` terminated with an error exit status (137)  

Command executed:  

  samtools view -q 1 -bh barcode01.bam | bedtools coverage -d -a TB_amplicons.bed -b - > barcode01.bedtools-coverage.bed  

Command exit status:  
  137  

Command output:  
  (empty)  

Command error:  
  .command.sh: line 2:    29 Broken pipe             samtools view -q 1 -bh barcode01.bam  
          30 Killed                  | bedtools coverage -d -a TB_amplicons.bed -b - > barcode01.bedtools-coverage.bed  

Work dir:  
  /home/hassan/epi2melabs/instances/wf-tb-amr_01JCGETWXPRWX7F3PFV8FZ5BMS/work/fc/d263ee6

[GenoMax]

Just to confirm. You are using barcoded samples and have provided a correct samplesheet file.

Answer 1

[jared.andrews07]

Exit code 137 is pretty much always a memory issue. The process is running out of RAM. Bump the amount for that process in your config.