Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX18040013_SRR22059179)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX18040013_SRR22059179)` terminated with an error exit status (1)


Command executed:

  export NCBI_SETTINGS="$PWD/user-settings.mkfg"
  
  fasterq-dump \
      --split-files --include-technical \
      --threads 6 \
      --outfile SRX18040013_SRR22059179 \
       \
      SRR22059179
  
  pigz \
       \
      --no-name \
      --processes 6 \
      *.fastq
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
      sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command wrapper:
  slurmstepd: error: *** JOB 22746559 ON n3185 CANCELLED AT 2024-12-05T15:48:09 DUE TO PREEMPTION ***
  /var/spool/slurmd/job22746559/slurm_script: line 305: pid: unbound variable

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20241205_FetchNGS/work/0f/9e08d294ce4a8dbf1456018e87b3c2

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`