Nextflow workflow report

[deadly_engelbart]

Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:SUB_EUKULELE:EUKULELE_SEARCH (megahit.prokka)'

Caused by:
  Process exceeded running time limit (16h)


Command executed:

  rc=0
  mkdir contigs
  gunzip -c prokka.faa.gz > ./contigs/proteins.faa
  EUKulele \
      -m mets \
       \
      --protein_extension .faa \
      --reference_dir db \
      -o megahit.prokka_[] \
      --CPUs 12 \
      -s \
      contigs || rc=$?
  
  gzip megahit.prokka_[]/mets_full/diamond/*.out
  find megahit.prokka_[]/ -name "*.csv" | xargs gzip
  gzip megahit.prokka_[]/taxonomy_estimation/*.out
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METATDENOVO:METATDENOVO:SUB_EUKULELE:EUKULELE_SEARCH":
      eukulele: $(echo $(EUKulele --version 2>&1) | sed -n 's/.* \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p')
  END_VERSIONS
  
  if [ $rc -le 1 ]; then
      exit 0
  else
      exit $rc;
  fi

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /home/nspmpego/microbiota_photoperiodism/metatranscriptomics/ld_sd_meta/work/f2/6ff4027d94eb82d726802074e2bd6d

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Run times

11-May-2026 13:35:03 - 13-May-2026 05:21:44 (duration: 1d 15h 46m 41s)

  146 succeeded  

  0 cached  

  0 ignored  

  1 failed (0 retries)  

Nextflow command

nextflow run nf-core/metatdenovo -profile conda --input samplesheet.csv --assembler megahit --save_bam --save_samtools --orf_caller prokka --eukulele_dbpath path/to/db /home/nspmpego/microbiota_photoperiodism/metatranscriptomics/eggnog/ --outdir results/ --email m.pegoraro@ljmu.ac.uk

CPU-Hours

634.5 (30.3% failed)

Launch directory

/home/nspmpego/microbiota_photoperiodism/metatranscriptomics/ld_sd_meta

Work directory

/home/nspmpego/microbiota_photoperiodism/metatranscriptomics/ld_sd_meta/work

Project directory

/home/nspmpego/.nextflow/assets/nf-core/metatdenovo

Script name

main.nf

Script ID

c5ed939ed357bbcf91b5c438297a9234

Workflow session

301de125-992f-4ee6-b5e7-07ec17b08b80

Workflow repository

https://github.com/nf-core/metatdenovo, revision master (commit hash 2a51399ef548164750563a4bf581fa25a39770f8)

Workflow profile

conda

Nextflow version

version 25.10.4, build 11173 (10-02-2026 15:17 UTC)