Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 2.

The full error message was:

Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)'

Caused by:
  Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)` terminated with an error exit status (2)


Command executed:

  # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
  # Check for container variable initialisation script and source it.
  if [ -f "/usr/local/env-activate.sh" ]; then
      set +u  # Otherwise, errors out because of various unbound variables
      . "/usr/local/env-activate.sh"
      set -u
  fi
  
  # If the augustus config directory is not writable, then copy to writeable area
  if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then
      # Create writable tmp directory for augustus
      AUG_CONF_DIR=$( mktemp -d -p $PWD )
      cp -r $AUGUSTUS_CONFIG_PATH/* $AUG_CONF_DIR
      export AUGUSTUS_CONFIG_PATH=$AUG_CONF_DIR
      echo "New AUGUSTUS_CONFIG_PATH=${AUGUSTUS_CONFIG_PATH}"
  fi
  
  # Ensure the input is uncompressed
  INPUT_SEQS=input_seqs
  mkdir "$INPUT_SEQS"
  cd "$INPUT_SEQS"
  for FASTA in ../tmp_input/*; do
      if [ "${FASTA##*.}" == 'gz' ]; then
          gzip -cdf "$FASTA" > $( basename "$FASTA" .gz )
      else
          ln -s "$FASTA" .
      fi
  done
  cd ..
  
  busco \
      --cpu 6 \
      --in "$INPUT_SEQS" \
      --out all_assembled--busco \
      --mode transcriptome \
      --lineage_dataset  \
       \
       \
  
  
  # clean up
  rm -rf "$INPUT_SEQS"
  
  # Move files to avoid staging/publishing issues
  mv all_assembled--busco/batch_summary.txt all_assembled--busco.batch_summary.txt
  mv all_assembled--busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO":
      busco: $( busco --version 2>&1 | sed 's/^BUSCO //' )
  END_VERSIONS

Command exit status:
  2

Command output:
  New AUGUSTUS_CONFIG_PATH=/gscratch/scrubbed/srlab/nxf.OnByylhFGt/tmp.CaFy5VTnmk

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
  usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
  busco: error: argument -l/--lineage_dataset: expected one argument

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/41/f7ae53efafe62ef07f9ec609aee385

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`