Error running pipeline with Nextflow 0.32.0

[edxxgardo]

Yesterday we ran the pipeline with the brand new version of Nextflow. In the attachment the error. We opened another issue when running the same pipeline: #93.

command_error_log.txt
nextflow.log.1.txt

[ewels]

ERROR ~ Error executing process > 'star (UHR_Rep2_ERCC-Mix1_1)'

Caused by:
  Not a valid memory value: null

Source block:
  prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
  def avail_mem = task.memory == null ? '' : "--limitBAMsortRAM ${task.memory.toBytes() - 100000000}"
  seqCenter = params.seqCenter ? "--outSAMattrRGline ID:$prefix 'CN:$params.seqCenter'" : ''
  """
  STAR --genomeDir $index \\
      --sjdbGTFfile $gtf \\
      --readFilesIn $reads  \\
      --runThreadN ${task.cpus} \\
      --twopassMode Basic \\
      --outWigType bedGraph \\
      --outSAMtype BAM SortedByCoordinate $avail_mem \\
      --readFilesCommand zcat \\
      --runDirPerm All_RWX \\
      --outFileNamePrefix $prefix $seqCenter \\
  """

@pditommaso, I guess this is being caused by the statement task.memory == null. Is this something that's changed in the last release? Should this code be replaced with something different?

[pditommaso]

This seems an issue on NF side, a possible and nicer workaround should be 👍

task.memory ? "--limitBAMsortRAM ${task.memory.toBytes() - 100000000 : ''

[ewels]

Updated and in PR #96 - tests now running. Thanks both!

[ewels]

Do you think that this will now be a problem?

rnaseq/conf/hebbe.config

Line 18 in acd1162

withName: '*' { memory = null }

[ewels]

Hi @edxxgardo,

I've just merged what I hope is a fix into the dev branch. If you could try running again and see if you still get the same problem, that would be great!

Thanks,

Phil

[edxxgardo]

Thanks. I'll try and get back to you soon.

[edxxgardo]

Ok, no more memory error. But, the problem with the never ending process mentioned in #93 is still there.

[ewels]

Great stuff, thanks! 🎉