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_METHYLSEQ:METHYLSEQ:FASTQC (EF07-EM01-Zygote)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:FASTQC (EF07-EM01-Zygote)` terminated with an error exit status (1)


Command executed:

  printf "%s %s\n" EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz EF07-EM01-Zygote_1.gz EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz EF07-EM01-Zygote_2.gz | while read old_name new_name; do
      [ -f "${new_name}" ] || ln -s $old_name $new_name
  done
  
  fastqc \
      --quiet \
      --threads 16 \
      --memory 6912 \
      EF07-EM01-Zygote_1.gz EF07-EM01-Zygote_2.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLSEQ:METHYLSEQ:FASTQC":
      fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
  END_VERSIONS

Command exit status:
  1

Command output:
  application/gzip
  application/gzip

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
  Failed to process file EF07-EM01-Zygote_2.gz
  uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Ran out of data in the middle of a fastq entry.  Your file is probably truncated
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:187)
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:129)
  	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
  	at java.base/java.lang.Thread.run(Thread.java:833)

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250502_methylseq/work/8a/09314e6973586447ae303df719dd7f

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img

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