Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 255.

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 (255)


Command executed:

  snpEff \
      -Xmx88473M \
      pmeandrina1 \
      [-c /gscratch/srlab/strigg/bin/snpEff/snpEff.config] \
      -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:
  255

Command output:
  (empty)

Command error:
  	-fastaProt                : Create an output file containing the resulting protein sequences.
  	-formatEff                      : Use 'EFF' field compatible with older versions (instead of 'ANN').
  	-geneId                         : Use gene ID instead of gene name (VCF output). Default: false
  	-hgvs                           : Use HGVS annotations for amino acid sub-field. Default: true
  	-hgvsOld                        : Use old HGVS notation. Default: false
  	-hgvs1LetterAa                  : Use one letter Amino acid codes in HGVS notation. Default: false
  	-hgvsTrId                       : Use transcript ID in HGVS notation. Default: false
  	-lof                            : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
  	-noHgvs                         : Do not add HGVS annotations.
  	-noLof                          : Do not add LOF and NMD annotations.
  	-noShiftHgvs                    : Do not shift variants according to HGVS notation (most 3prime end).
  	-oicr                           : Add OICR tag in VCF file. Default: false
  	-sequenceOntology               : Use Sequence Ontology terms. Default: true
  
  Generic options:
  	-c , -config                 : Specify config file
  	-configOption name=value     : Override a config file option
  	-d , -debug                  : Debug mode (very verbose).
  	-dataDir               : Override data_dir parameter from config file.
  	-download                    : Download a SnpEff database, if not available locally. Default: true
  	-nodownload                  : Do not download a SnpEff database, if not available locally.
  	-h , -help                   : Show this help and exit
  	-noLog                       : Do not report usage statistics to server
  	-q , -quiet                  : Quiet mode (do not show any messages or errors)
  	-v , -verbose                : Verbose mode
  	-version                     : Show version number and exit
  
  Database options:
  	-canon                       : Only use canonical transcripts.
  	-canonList             : Only use canonical transcripts, replace some transcripts using the 'gene_id 	 transcript_id' entries in .
  	-interaction                 : Annotate using inteactions (requires interaciton database). Default: true
  	-interval              : Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)
  	-maxTSL          : Only use transcripts having Transcript Support Level lower than .
  	-motif                       : Annotate using motifs (requires Motif database). Default: true
  	-nextProt                    : Annotate using NextProt (requires NextProt database).
  	-noGenome                    : Do not load any genomic database (e.g. annotate using custom files).
  	-noExpandIUB                 : Disable IUB code expansion in input variants
  	-noInteraction               : Disable inteaction annotations
  	-noMotif                     : Disable motif annotations.
  	-noNextProt                  : Disable NextProt annotations.
  	-onlyReg                     : Only use regulation tracks.
  	-onlyProtein                 : Only use protein coding transcripts. Default: false
  	-onlyTr            : Only use the transcripts in this file. Format: One transcript ID per line.
  	-reg                   : Regulation track to use (this option can be used add several times).
  	-ss , -spliceSiteSize   : Set size for splice sites (donor and acceptor) in bases. Default: 2
  	-spliceRegionExonSize   : Set size for splice site region within exons. Default: 3 bases
  	-spliceRegionIntronMin  : Set minimum number of bases for splice site region within intron. Default: 3 bases
  	-spliceRegionIntronMax  : Set maximum number of bases for splice site region within intron. Default: 8 bases
  	-strict                      : Only use 'validated' transcripts (i.e. sequence has been checked). Default: false
  	-ud , -upDownStreamLen  : Set upstream downstream interval length (in bases)

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250721_rnavar/work/68/e5108f7720819a9d50d0abcb5c190c

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`