Memory issue

[JohnHellgren]

Hello,

I think there's a problem with the memory allocation of Trim galore (and possibly the other steps):

rnaseq/conf/hebbe.config

Line 23 in 18849b0

withName:trim_galore.memory = null

I get this error when I run the 1.1.hebbe pipeline:

[14/b77668] NOTE: Error submitting process 'trim_galore (E1_S9_L001)' for execution -- Execution is retried (2)
[95/49aaee] NOTE: Error submitting process 'trim_galore (E1_S9_L001)' for execution -- Execution is retried (3)
ERROR ~ Error executing process > 'trim_galore (E1_S9_L001)'

Caused by:
  Failed to submit process to grid scheduler for execution

Command executed:

  sbatch .command.run

Command exit status:
  1

Command output:
  sbatch: error: rejecting job, too much memory requested for 2 cores. You must use -C MEMXXX or increase number of requested cores instead of using --mem: pn_min_memory = 65536
  sbatch: error: Batch job submission failed: Invalid generic resource (gres) specification

It's fixed by adding this to the config_TEMPLATE:

process {
memory = null
  withName:makeSTARindex { memory = null }
  withName:makeHisatSplicesites { memory = null }
  withName:makeHISATindex { memory = null }
  withName:fastqc { memory = null }
  withName:trim_galore { memory = null }
  withName:star { memory = null }
  withName:hisat2Align { memory = null }
  withName:hisat2_sortOutput { memory = null }
  withName:rseqc { memory = null }
  withName:genebody_coverage { memory = null }
  withName:preseq { memory = null }
  withName:markDuplicates { memory = null }
  withName:dupradar { memory = null }
  withName:featureCounts { memory = null }
  withName:merge_featureCounts { memory = null }
  withName:stringtieFPKM { memory = null }
  withName:sample_correlation { memory = null }
  withName:multiqc { memory = null }
}

Maybe the withName syntax is wrong in the hebbe.config?
I assume that what I write in the config_TEMPLATE overwrites what's stated in the hebbe.config

I ran revision: [0dc48d498f 1.1.hebbe]

[mihai-sysbio]

Indeed the hebbe.config syntax is wrong, confirmed by nf-core#82 (comment) .