Nextflow workflow report

[sleepy_feynman]

Error executing process > 'SNPS:preprocessing (sample5)'

Caused by:
  Process `SNPS:preprocessing (sample5)` terminated with an error exit status (127)

Command executed:

  samtools sort -T deleteme -m 966367642 -@ 4 \
  -o sorted.bam sample5.bam || exit $?
  samtools calmd -b sorted.bam genome.fa 1> calmd.bam 2> /dev/null && rm sorted.bam
  samtools index calmd.bam

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: samtools: command not found

Work dir:
  /home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code/work/4a/4f7f9e484fea495ec4b580b7cf7df5

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Run times

19-Jun-2022 09:16:37 - 19-Jun-2022 09:16:53 (duration: 15.5s)

  0 succeeded  

  0 cached  

  0 ignored  

  12 failed  

Nextflow command

nextflow run epidiverse/snp -profile test, docker

CPU-Hours

(a few seconds)

Launch directory

/home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code

Work directory

/home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code/work

Project directory

/home/sr320/.nextflow/assets/epidiverse/snp

Script name

main.nf

Script ID

b0e299ed332648922c66d8a020a05bca

Workflow session

7eff3b25-c302-448c-a254-4c06ce498dce

Workflow repository

https://github.com/epidiverse/snp, revision master (commit hash 9c814703c690c2ade21c4586b36159940e092a4e)

Workflow profile

test,

Nextflow version

version 22.04.3, build 5703 (18-05-2022 19:22 UTC)