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