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_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (POC-201-TP1)'

Caused by:
  Process `NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (POC-201-TP1)` terminated with an error exit status (1)


Command executed:

  snpEff \
      -Xmx88473M \
      pmeandrina1 \
      -configOption pmeandrina1.genome: P_meandrina \
      -csvStats POC-201-TP1.csv \
      -dataDir ${PWD}/data \
      POC-201-TP1.haplotypecaller.filtered.vcf.gz \
      > POC-201-TP1.ann.vcf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF":
      snpeff: $(echo $(snpEff -version 2>&1) | cut -f 2 -d ' ')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
  	at org.snpeff.SnpEff.parseArgs(SnpEff.java:907)
  	at org.snpeff.SnpEff.cmd(SnpEff.java:229)
  	at org.snpeff.SnpEff.run(SnpEff.java:1134)
  	at org.snpeff.SnpEff.main(SnpEff.java:160)

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250721_rnavar/work/a9/f538917103699b2e1d2dae0ff15587

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-snpeff-5.1--hdfd78af_2.img

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`