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_METHYLSEQ:FASTA_INDEX_BISMARK_BWAMETH:BISMARK_GENOMEPREPARATION (BismarkIndex/GCF_031168955.1_ASM3116895v1_genomic.fna)'

Caused by:
  Process `NFCORE_METHYLSEQ:FASTA_INDEX_BISMARK_BWAMETH:BISMARK_GENOMEPREPARATION (BismarkIndex/GCF_031168955.1_ASM3116895v1_genomic.fna)` terminated with an error exit status (255)


Command executed:

  bismark_genome_preparation \
      --bowtie2 \
      BismarkIndex
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLSEQ:FASTA_INDEX_BISMARK_BWAMETH:BISMARK_GENOMEPREPARATION":
      bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
  END_VERSIONS

Command exit status:
  255

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
  Writing bisulfite genomes out into a single MFA (multi FastA) file
  
  The specified genome folder /gscratch/scrubbed/srlab/nxf.C73Xfo0L1Y/BismarkIndex/ does not contain any sequence files in FastA format (with .fa, .fa.gz, .fasta or .fasta.gz file extensions)

Work dir:
  /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/17-nextflow/work/cb/b4af45e1e0dca774f79072d911f2f0

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-bismark-0.24.2--hdfd78af_0.img

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