----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~\
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/metatdenovo v1.1-g78689bd
----------------------------------------------------
Run Name: serene_euclid

####################################################
## nf-core/metatdenovo 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_METATDENOVO:METATDENOVO:SUB_EUKULELE:EUKULELE_SEARCH (megahit.prokka)'

Caused by:
  Process `NFCORE_METATDENOVO:METATDENOVO:SUB_EUKULELE:EUKULELE_SEARCH (megahit.prokka)` terminated with an error exit status (1)


Command executed:

  rc=0
  mkdir contigs
  gunzip -c prokka.faa.gz > ./contigs/proteins.faa
  EUKulele \
      -m mets \
      --database gtdb \
      --protein_extension .faa \
      --reference_dir eukulele \
      -o megahit.prokka \
      --CPUs 12 \
      -s \
      contigs || rc=$?
  
  gzip megahit.prokka/mets_full/diamond/*.out
  gzip megahit.prokka/taxonomy_counts/*.csv
  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:
  1

Command output:
  All reference files for GTDB downloaded to eukulele/gtdb
  Running EUKulele with command line arguments, as no valid configuration file was provided.
  Setting things up...
  Could not successfully install all external dependent software.
  Check DIAMOND, BLAST, BUSCO, and TransDecoder installation.
  ['proteins']
  Specified reference directory, reference FASTA, and protein map/taxonomy table not found. Using database in location: eukulele/gtdb.
  Automatically downloading database gtdb . If you intended to use an existing database folder, be sure a reference FASTA, protein map, and taxonomy table are provided. Check the documentation for details.

Command error:
    5900K .......... .......... .......... .......... .......... 72% 34.0M 0s
    5950K .......... .......... .......... .......... .......... 73% 53.0M 0s
    6000K .......... .......... .......... .......... .......... 74% 34.5M 0s
    6050K .......... .......... .......... .......... .......... 74% 34.5M 0s
    6100K .......... .......... .......... .......... .......... 75%  936K 0s
    6150K .......... .......... .......... .......... .......... 76% 44.9M 0s
    6200K .......... .......... .......... .......... .......... 76% 68.3M 0s
    6250K .......... .......... .......... .......... .......... 77% 45.6M 0s
    6300K .......... .......... .......... .......... .......... 77% 63.5M 0s
    6350K .......... .......... .......... .......... .......... 78% 41.3M 0s
    6400K .......... .......... .......... .......... .......... 79% 46.6M 0s
    6450K .......... .......... .......... .......... .......... 79% 54.0M 0s
    6500K .......... .......... .......... .......... .......... 80% 71.3M 0s
    6550K .......... .......... .......... .......... .......... 80% 49.0M 0s
    6600K .......... .......... .......... .......... .......... 81% 54.1M 0s
    6650K .......... .......... .......... .......... .......... 82% 51.0M 0s
    6700K .......... .......... .......... .......... .......... 82% 82.6M 0s
    6750K .......... .......... .......... .......... .......... 83% 50.0M 0s
    6800K .......... .......... .......... .......... .......... 84% 52.2M 0s
    6850K .......... .......... .......... .......... .......... 84% 42.7M 0s
    6900K .......... .......... .......... .......... .......... 85% 84.8M 0s
    6950K .......... .......... .......... .......... .......... 85% 68.0M 0s
    7000K .......... .......... .......... .......... .......... 86% 46.0M 0s
    7050K .......... .......... .......... .......... .......... 87% 47.3M 0s
    7100K .......... .......... .......... .......... .......... 87% 83.1M 0s
    7150K .......... .......... .......... .......... .......... 88% 76.9M 0s
    7200K .......... .......... .......... .......... .......... 88% 51.1M 0s
    7250K .......... .......... .......... .......... .......... 89% 61.2M 0s
    7300K .......... .......... .......... .......... .......... 90% 52.9M 0s
    7350K .......... .......... .......... .......... .......... 90% 80.7M 0s
    7400K .......... .......... .......... .......... .......... 91% 59.2M 0s
    7450K .......... .......... .......... .......... .......... 92% 55.2M 0s
    7500K .......... .......... .......... .......... .......... 92% 45.3M 0s
    7550K .......... .......... .......... .......... .......... 93% 36.4M 0s
    7600K .......... .......... .......... .......... .......... 93% 59.5M 0s
    7650K .......... .......... .......... .......... .......... 94% 71.2M 0s
    7700K .......... .......... .......... .......... .......... 95% 84.9M 0s
    7750K .......... .......... .......... .......... .......... 95% 64.7M 0s
    7800K .......... .......... .......... .......... .......... 96% 80.7M 0s
    7850K .......... .......... .......... .......... .......... 96% 70.1M 0s
    7900K .......... .......... .......... .......... .......... 97% 83.1M 0s
    7950K .......... .......... .......... .......... .......... 98% 70.9M 0s
    8000K .......... .......... .......... .......... .......... 98% 53.3M 0s
    8050K .......... .......... .......... .......... .......... 99% 67.0M 0s
    8100K .......... .......... .......... .......... .......... 99% 88.7M 0s
    8150K                                                       100% 1.76T=0.5s
  
  2024-10-29 11:07:32 (14.9 MB/s) - ‘eukulele/gtdb/taxonomy-table.txt’ saved [8346567/8346567]
  
  gzip: megahit.prokka/mets_full/diamond/*.out: No such file or directory

Work dir:
  /crex/proj/naiss2023-23-158/nobackup/projects/sas-metatdenovo/work/53/9bb22ef66fd2fb867b52bf31231864

Container:
  /proj/sllstore2017037/nobackup/emelie/singularity_cache/depot.galaxyproject.org-singularity-eukulele-2.0.5--pyh723bec7_0.img

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



The workflow was completed at 2024-10-29T13:47:07.369105+01:00 (duration: 3h 48m 37s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/metatdenovo -r dev -profile uppmax -params-file params.yaml -resume



Pipeline Configuration:
-----------------------
 - revision: dev
 - runName: serene_euclid
 - containerEngine: singularity
 - launchDir: /crex/proj/naiss2023-23-158/nobackup/projects/sas-metatdenovo
 - workDir: /crex/proj/naiss2023-23-158/nobackup/projects/sas-metatdenovo/work
 - projectDir: /home/geweaa/.nextflow/assets/nf-core/metatdenovo
 - userName: geweaa
 - profile: uppmax
 - configFiles: 
 - input: input.csv
 - outdir: output
 - email: george.westmeijer@umu.se
 - sequence_filter: /proj/sllstore2017037/nobackup/emelie/SILVA_138.1_allrRNAref_NR99_tax.fasta
 - orf_caller: prokka
 - eggnog_dbpath: /proj/snic2020-16-76/nobackup/data/eggnog-mapper/
 - skip_kofamscan: true
 - eukulele_db: gtdb
 - config_profile_description: UPPMAX (Rackham) cluster profile provided by nf-core/configs.
 - config_profile_contact: Phil Ewels (@ewels)
 - config_profile_url: https://www.uppmax.uu.se/
 - max_cpus: 20
 - max_memory: 970 GB
 - max_time: 10d
 - Date Started: 2024-10-29T09:58:30.081031+01:00
 - Date Completed: 2024-10-29T13:47:07.369105+01:00
 - Pipeline script file path: /home/geweaa/.nextflow/assets/nf-core/metatdenovo/main.nf
 - Pipeline script hash ID: 807e872512cdbc1250215e3df4264ab5
 - Pipeline repository Git URL: https://github.com/nf-core/metatdenovo
 - Pipeline repository Git Commit: 78689bdfe9fe1226d2057bf32450e239ed2aeb8d
 - Pipeline Git branch/tag: dev
 - Nextflow Version: 24.10.0
 - Nextflow Build: 5928
 - Nextflow Compile Timestamp: 27-10-2024 18:36 UTC

--
nf-core/metatdenovo
https://github.com/nf-core/metatdenovo
