Run_Kallisto_for_quantification terminated with an error exit status (137)

[peris...@nevada.unr.edu]

I am currently trying to run this Nextflow pipeline (https://github.com/likelet/LncPipe) using a Docker image and I encountered the following error:

```

Aug-08 20:18:35.603 [Task monitor] ERROR nextflow.processor.TaskProcessor - Erro
r executing process > 'Run_kallisto_for_quantification (AAhu-FFinfer-TTsp-SS2)'

Caused by:
  Process `Run_kallisto_for_quantification (AAhu-FFinfer-TTsp-SS2)` terminated with an error exit status (137)

Command executed:

  #quantification by kallisto
  kallisto quant -i transcripts.idx -o AAhu-FFinfer-TTsp-SS2_kallisto -t 23 -b 100 AAhu-FFinfer-TTsp-SS2.R1.fq.gz AAhu-FFinfer-TTsp-SS2.R2.fq.gz
  mv AAhu-FFinfer-TTsp-SS2_kallisto/abundance.tsv AAhu-FFinfer-TTsp-SS2_abundance.tsv

Command exit status:
  137

Command output:
  (empty)

Command error:
 
  [quant] fragment length distribution will be estimated from the data
  [index] k-mer length: 31
  [index] number of targets: 213,479
  [index] number of k-mers: 614,018,229
  [index] number of equivalence classes: 3,877,325
  .command.sh: line 3:     9 Killed                  kallisto quant -i transcripts.idx -o AAhu-FFinfer-TTsp-SS2_kallisto -t 23 -b 100 AAhu-FFinfer-TTsp-SS2.R1.fq.gz AAhu-FFinfer-TTsp-SS2.R2.fq.gz

```

Any inputs on debugging this would be much appreciated.

Thank You

[Paolo Di Tommaso]

Exit status 137 is usually caused by lack of memory. To debug any task change in the task work directory and execute `bash .command.run` 

Hope it helps. 

p

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[peris...@nevada.unr.edu]

It was indeed a memory segmentation issue...was able to fix it in the nextflow.config file.

TY

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