Prokka: contig length too long - add option for `--compliant` mode

[audy]

Description of the bug

I am running nf-core/mag 3.0.3 on a sample (ERR4303137) and it fails during the Prokka step.

This looks like it might be a simple fix (adding --compliant --centre-name something) but I'm not sure what the downstream effects will be.

Command used and terminal output

nextflow run main.nf \
  --input input.csv \
  --outdir output-test

Terminal output:

(click to expand)

ERROR ~ Error executing process > 'NFCORE_MAG:MAG:PROKKA (SPAdes-MaxBin2-ERR4303137.013)'

Caused by:
  Process `NFCORE_MAG:MAG:PROKKA (SPAdes-MaxBin2-ERR4303137.013)` terminated with an error exit status (2)


Command executed:

  prokka \
      --metagenome \
      --cpus 2 \
      --prefix SPAdes-MaxBin2-ERR4303137.013 \
       \
       \
      SPAdes-MaxBin2-ERR4303137.013.fa
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:PROKKA":
      prokka: $(echo $(prokka --version 2>&1) | sed 's/^.*prokka //')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  [21:14:52] You are not telling me who you are!
  [21:14:52] Operating system is linux
  [21:14:52] You have BioPerl 1.7.8
  Argument "1.7.8" isn't numeric in numeric lt (<) at /usr/local/bin/prokka line 259.
  [21:14:52] System has 32 cores.
  [21:14:52] Will use maximum of 2 cores.
  [21:14:52] Annotating as >>> Bacteria <<<
  [21:14:52] Generating locus_tag from 'SPAdes-MaxBin2-ERR4303137.013.fa' contents.
  [21:14:52] Setting --locustag ALGKCLFE from MD5 a504c5fe5e1f9958c5675ed865168409
  [21:14:52] Creating new output folder: SPAdes-MaxBin2-ERR4303137.013
  [21:14:52] Running: mkdir -p SPAdes\-MaxBin2\-ERR4303137\.013
  [21:14:52] Using filename prefix: SPAdes-MaxBin2-ERR4303137.013.XXX
  [21:14:52] Setting HMMER_NCPU=1
  [21:14:52] Writing log to: SPAdes-MaxBin2-ERR4303137.013/SPAdes-MaxBin2-ERR4303137.013.log
  [21:14:52] Command: /usr/local/bin/prokka --metagenome --cpus 2 --prefix SPAdes-MaxBin2-ERR4303137.013 SPAdes-MaxBin2-ERR4303137.013.fa
  [21:14:52] Appending to PATH: /usr/local/bin
  [21:14:52] Looking for 'aragorn' - found /usr/local/bin/aragorn
  [21:14:52] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
  [21:14:52] Looking for 'barrnap' - found /usr/local/bin/barrnap
  [21:14:52] Determined barrnap version is 000009 from 'barrnap 0.9'
  [21:14:52] Looking for 'blastp' - found /usr/local/bin/blastp
  [21:14:52] Determined blastp version is 002012 from 'blastp: 2.12.0+'
  [21:14:52] Looking for 'cmpress' - found /usr/local/bin/cmpress
  [21:14:52] Determined cmpress version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)'
  [21:14:52] Looking for 'cmscan' - found /usr/local/bin/cmscan
  [21:14:52] Determined cmscan version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)'
  [21:14:52] Looking for 'egrep' - found /bin/egrep
  [21:14:52] Looking for 'find' - found /usr/bin/find
  [21:14:52] Looking for 'grep' - found /bin/grep
  [21:14:52] Looking for 'hmmpress' - found /usr/local/bin/hmmpress
  [21:14:52] Determined hmmpress version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/'
  [21:14:52] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
  [21:14:52] Determined hmmscan version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/'
  [21:14:52] Looking for 'java' - found /usr/local/bin/java
  [21:14:52] Looking for 'makeblastdb' - found /usr/local/bin/makeblastdb
  [21:14:52] Determined makeblastdb version is 002012 from 'makeblastdb: 2.12.0+'
  [21:14:52] Looking for 'minced' - found /usr/local/bin/minced
  [21:14:52] Determined minced version is 004002 from 'minced 0.4.2'
  [21:14:52] Looking for 'parallel' - found /usr/local/bin/parallel
  [21:14:52] Determined parallel version is 20220222 from 'GNU parallel 20220222'
  [21:14:52] Looking for 'prodigal' - found /usr/local/bin/prodigal
  [21:14:52] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
  [21:14:52] Looking for 'prokka-genbank_to_fasta_db' - found /usr/local/bin/prokka-genbank_to_fasta_db
  [21:14:52] Looking for 'sed' - found /bin/sed
  [21:14:52] Looking for 'tbl2asn' - found /usr/local/bin/tbl2asn
  [21:14:52] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
  [21:14:52] Using genetic code table 11.
  [21:14:52] Loading and checking input file: SPAdes-MaxBin2-ERR4303137.013.fa
  [21:14:53] Contig ID must <= 37 chars long: NODE_37914_length_1491_cov_1063.826602
  [21:14:53] Please rename your contigs OR try '--centre X --compliant' to generate clean contig names.

Relevant files

No response

System information

• Nextflow 24.04.2
• Hardware: cloud
• Executor: TES
• Container engine: Docker
• OS: Ubuntu
• Version of nf-core/mag: 3.0.3