Issue running pipeline on AWS Batch

[prmac]

Trying to run RNAseq pipeline with test dataset and version 20.07.1

nextflow run nf-core/rnaseq -profile test,awsbatch,docker -c aws.config -bucket-dir s3://test_bucket/nf-work/ -r f029b7d3cc7ea055fd3f26795c2237a95cfcfe8f

Results in the following error

Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (127)

Command executed:

  echo 1.4.3dev &> v_ngi_rnaseq.txt
  echo 20.07.1 &> v_nextflow.txt
  fastqc --version &> v_fastqc.txt
  cutadapt --version &> v_cutadapt.txt
  trim_galore --version &> v_trim_galore.txt
  sortmerna --version &> v_sortmerna.txt
  STAR --version &> v_star.txt
  hisat2 --version &> v_hisat2.txt
  stringtie --version &> v_stringtie.txt
  preseq &> v_preseq.txt
  read_duplication.py --version &> v_rseqc.txt
  bamCoverage --version &> v_deeptools.txt || true
  featureCounts -v &> v_featurecounts.txt
  rsem-calculate-expression --version &> v_rsem.txt
  salmon --version &> v_salmon.txt
  picard MarkDuplicates --version &> v_markduplicates.txt  || true
  samtools --version &> v_samtools.txt
  multiqc --version &> v_multiqc.txt
  Rscript -e "library(edgeR); write(x=as.character(packageVersion('edgeR')), file='v_edgeR.txt')"
  Rscript -e "library(dupRadar); write(x=as.character(packageVersion('dupRadar')), file='v_dupRadar.txt')"
  unset DISPLAY && qualimap rnaseq &> v_qualimap.txt || true
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  127

Command output:
  (empty)

Command wrapper:
  nxf-scratch-dir ip-10-0-61-240:/tmp/nxf.XVPPKt4Wd9

[drpatelh]

Hi @prmac ! I am assuming you managed to resolve the issue? Just out of interest what worked for you?

[drpatelh]

I ask because #500 would indicate there is a bug in the logic for the awsbatch profile. But if it's working for you then that may not be the case. Still need to test it all properly.

[prmac]

Hi @drpatelh it was a problem with my Conda environment and running an old version of nextflow.
I did come across another problem though. I'll open a new issue.