These are chat archives for nextflow-io/nextflow

31st
Jan 2019
lastwon1216
@lastwon1216
Jan 31 00:46
i changed my scripts in many ways to get this work, it wouldn't take a single parameter and give out an error with unbound variable without any explanation even if I set it in my command line..
scalavision
@scalavision
Jan 31 09:46
Hello, is there a similar nextflow variable like workDir for the path the script itself is running from, i.e. I am thinking about the path work/a0/<some hash code>/<this location>
I would like to know this directly from nextflow, not having to do some \$(pwd) or something in the script.
Yasset Perez-Riverol
@ypriverol
Jan 31 10:53
Hi everyone, my current workflow is failig because nextflow (I think is killing the job). here the output
Command exit status:
  247

Command output:
  Path configuration completed.
  Thu Jan 31 10:44:09 GMT 2019 Unzipping crap-test.mgf.zip.
  10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

  Thu Jan 31 10:44:17 GMT 2019 Import process for myExperiment (Sample: mySample, Replicate: 1)

  Thu Jan 31 10:44:17 GMT 2019 Importing sequences from db_concatenated_target_decoy.fasta.
  Reindexing: db_concatenated_target_decoy.fasta.
  10% 20% 30% 40% 50% 60% 70% 80% 90%
  Thu Jan 31 10:44:23 GMT 2019 Estimated import time: 5 minutes.
  Thu Jan 31 10:44:23 GMT 2019     See http://compomics.github.io/projects/compomics-utilities/wiki/proteininference.html.

Command error:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/usr/local/share/peptide-shaker-1.16.36-0/lib/gson-2.4.jar) to field java.awt.Color.value
  WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
I have added 247 as validExitStatus 247 but the job is still kill.
Rad Suchecki
@rsuchecki
Jan 31 10:56
@scalavision task.workDir
micans
@micans
Jan 31 10:57
@lastwon1216 for debugging, go into the work directory and have a look at the file .command.sh. Second, the line prefix="sed 's/.fastq//' ${params.reads}" is not doing what you want it to do. It just sets prefix to a weird string.
Paolo Di Tommaso
@pditommaso
Jan 31 11:00
@ypriverol 247 it's a very unusual exit code, are you using a cluster to run it?
Yasset Perez-Riverol
@ypriverol
Jan 31 11:00
locally, this is because java inside the container is throwing it
Paolo Di Tommaso
@pditommaso
Jan 31 11:01
this looks some kind of mess of java heap and container memory
Yasset Perez-Riverol
@ypriverol
Jan 31 11:02
ok let me check
Paolo Di Tommaso
@pditommaso
Jan 31 11:02
also this
micans
@micans
Jan 31 14:59

@pditommaso can we run this by you (k8s error):

kingfisher,d7/2a6149b458a5a11aa077699bc55769 :-() cat .command.log
touch: cannot touch '/workspace/svd/drop/work/d7/2a6149b458a5a11aa077699bc55769/.command.begin': Permission denied
.command.run: line 36: /workspace/svd/drop/work/d7/2a6149b458a5a11aa077699bc55769/.exitcode: Permission denied

Other steps in the pipeline work, this one fails; it seems related to the docker image; do you have a hunch what it could be?

lastwon1216
@lastwon1216
Jan 31 17:29
@micans the issue is that this is all I am getting from .commnd.sh... can't fine reason why it is giving me that error:

#!/bin/bash -ue
/common/genomics-core/anaconda2/bin/STAR         --readFilesIn ${reads}         --genomeDir ${genome}         --outSAMmode Full         --outSAMunmapped Within         --readFilesCommand zcat         --outFilterType Normal         --outSAMattributes All         --outFilterMultimapNmax 20         --outFilterMismatchNmax 999         --outFilterMismatchNoverLmax 0.04         --alignIntronMin 20         --alignIntronMax 1000000         --alignMatesGapMax 1000000         --alignSJoverhangMin 8         --alignSJDBoverhangMin 1         --sjdbScore 1         --runThreadN 3         --genomeLoad LoadAndKeep         --limitBAMsortRAM 10000000002         --outSAMtype BAM SortedByCoordinate         --quantMode TranscriptomeSAM         --outFileNamePrefix ${prefix}
Hyunmin Kim (Brandon)
@hmkim
Jan 31 23:29
Hi, All.