Nextflow workflow report

[tender_cray]

Error executing process > 'SNPS:masking (zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted - variants)'

Caused by:
  Process exceeded running time limit (4h)

Command executed:

  change_sam_queries.py -Q -T 16 -t . calmd.bam variants.bam || exit $?
  find -mindepth 1 -maxdepth 1 -type d -exec rm -r {} \;

Command exit status:
  -

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

Work dir:
  /home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/code/work/a1/abbf9727bef790aa88811ab8cd9974

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

06-Jul-2022 17:11:53 - 07-Jul-2022 07:01:36 (duration: 13h 49m 43s)

  10 succeeded  

  0 cached  

  0 ignored  

  23 failed  

Nextflow command

nextflow run epidiverse/snp -c nfx.config -profile docker --input ../data/bgdata/ --reference ../data/bgdata/Olurida_v081.fa

CPU-Hours

516.4 (99.2% failed)

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

3dce6940-f803-49e6-a782-dac251a941d8

Workflow repository

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

Workflow profile

docker

Workflow container

epidiverse/snp:1.0

Container engine

docker

Nextflow version

version 20.07.1, build 5412 (24-07-2020 15:18 UTC)