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_MAG:MAG:PROKKA (SPAdes-CONCOCT-CR180008_149)'

Caused by:
  Process `NFCORE_MAG:MAG:PROKKA (SPAdes-CONCOCT-CR180008_149)` terminated with an error exit status (2)


Command executed:

  prokka \
      --metagenome \
      --cpus 2 \
      --prefix SPAdes-CONCOCT-CR180008_149 \
       \
       \
      SPAdes-CONCOCT-CR180008_149.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:
  [10:36:10] You are not telling me who you are!
  [10:36:10] Operating system is linux
  [10:36:10] You have BioPerl 1.7.8
  Argument "1.7.8" isn't numeric in numeric lt (<) at /opt/conda/bin/prokka line 259.
  [10:36:10] System has 64 cores.
  [10:36:10] Will use maximum of 2 cores.
  [10:36:10] Annotating as >>> Bacteria <<<
  [10:36:10] Generating locus_tag from 'SPAdes-CONCOCT-CR180008_149.fa' contents.
  [10:36:10] Setting --locustag AMJKICIC from MD5 a6342c2cb1e6d068a54207870eea78bb
  [10:36:10] Creating new output folder: SPAdes-CONCOCT-CR180008_149
  [10:36:10] Running: mkdir -p SPAdes\-CONCOCT\-CR180008_149
  [10:36:10] Using filename prefix: SPAdes-CONCOCT-CR180008_149.XXX
  [10:36:10] Setting HMMER_NCPU=1
  [10:36:10] Writing log to: SPAdes-CONCOCT-CR180008_149/SPAdes-CONCOCT-CR180008_149.log
  [10:36:10] Command: /opt/conda/bin/prokka --metagenome --cpus 2 --prefix SPAdes-CONCOCT-CR180008_149 SPAdes-CONCOCT-CR180008_149.fa
  [10:36:10] Appending to PATH: /opt/conda/bin
  [10:36:10] Looking for 'aragorn' - found /opt/conda/bin/aragorn
  [10:36:10] Determined aragorn version is 001002 from 'ARAGORN v1.2.41 Dean Laslett'
  [10:36:10] Looking for 'barrnap' - found /opt/conda/bin/barrnap
  [10:36:10] Determined barrnap version is 000009 from 'barrnap 0.9'
  [10:36:10] Looking for 'blastp' - found /opt/conda/bin/blastp
  [10:36:10] Determined blastp version is 002016 from 'blastp: 2.16.0+'
  [10:36:10] Looking for 'cmpress' - found /opt/conda/bin/cmpress
  [10:36:10] Determined cmpress version is 001001 from '# INFERNAL 1.1.5 (Sep 2023)'
  [10:36:10] Looking for 'cmscan' - found /opt/conda/bin/cmscan
  [10:36:10] Determined cmscan version is 001001 from '# INFERNAL 1.1.5 (Sep 2023)'
  [10:36:10] Looking for 'egrep' - found /usr/bin/egrep
  [10:36:10] Looking for 'find' - found /usr/bin/find
  [10:36:10] Looking for 'grep' - found /usr/bin/grep
  [10:36:10] Looking for 'hmmpress' - found /opt/conda/bin/hmmpress
  [10:36:10] Determined hmmpress version is 003004 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
  [10:36:10] Looking for 'hmmscan' - found /opt/conda/bin/hmmscan
  [10:36:10] Determined hmmscan version is 003004 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/'
  [10:36:10] Looking for 'java' - found /opt/conda/bin/java
  [10:36:10] Looking for 'makeblastdb' - found /opt/conda/bin/makeblastdb
  [10:36:10] Determined makeblastdb version is 002016 from 'makeblastdb: 2.16.0+'
  [10:36:10] Looking for 'minced' - found /opt/conda/bin/minced
  [10:36:11] Determined minced version is 004002 from 'minced 0.4.2'
  [10:36:11] Looking for 'parallel' - found /opt/conda/bin/parallel
  [10:36:11] Determined parallel version is 20241122 from 'GNU parallel 20241122'
  [10:36:11] Looking for 'prodigal' - found /opt/conda/bin/prodigal
  [10:36:11] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
  [10:36:11] Looking for 'prokka-genbank_to_fasta_db' - found /opt/conda/bin/prokka-genbank_to_fasta_db
  [10:36:11] Looking for 'sed' - found /usr/bin/sed
  [10:36:11] Looking for 'tbl2asn' - found /opt/conda/bin/tbl2asn
  [10:36:11] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
  [10:36:11] Using genetic code table 11.
  [10:36:11] Loading and checking input file: SPAdes-CONCOCT-CR180008_149.fa
  [10:36:11] Contig ID must <= 37 chars long: NODE_13554_length_2509_cov_1572.037897
  [10:36:11] Please rename your contigs OR try '--centre X --compliant' to generate clean contig names.

Work dir:
  /project2/ckenkel_26/liruiqi/mag_out_project2/docker_withhost/work/55/2a7a96a0452ad09f8091121018e366

Container:
  /project2/ckenkel_26/liruiqi/mag_out_project2/docker_withhost/work/singularity/community.wave.seqera.io-library-prokka_openjdk-10546cadeef11472.img

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`