Nextflow workflow report

Workflow 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_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF (SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi)'

Caused by:
  Process `NFCORE_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF (SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi)` terminated with an error exit status (1)


Command executed:

  export GTDBTK_DATA_PATH="$(find -L gtdb -name 'metadata' -type d -exec dirname {} \;)"
  
  if [ "--scratch_dir pplacer_tmp" != "" ] ; then
      mkdir pplacer_tmp
  fi
  
  gtdbtk classify_wf \
      --extension fa --min_perc_aa 10 --min_af 0.65 --pplacer_cpus 1   \
      --genome_dir bins \
      --prefix "SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi" \
      --out_dir SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi \
      --cpus 30 \
      --scratch_dir pplacer_tmp
  
  mv SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi/gtdbtk.log "SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi/SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi.log"
  mv SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi/gtdbtk.warnings.log "SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi/SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi.warnings.log"
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:GTDBTK:GTDBTK_CLASSIFYWF":
      gtdbtk: $(echo $(gtdbtk --version 2>/dev/null) | sed "s/gtdbtk: version //; s/ Copyright.*//")
      gtdb_db: $(grep VERSION_DATA $GTDBTK_DATA_PATH/metadata/metadata.txt | sed "s/VERSION_DATA=//")
  END_VERSIONS

Command exit status:
  1

Command output:
  [2026-03-05 19:16:44] INFO: GTDB-Tk v2.5.2
  [2026-03-05 19:16:44] INFO: gtdbtk classify_wf --extension fa --min_perc_aa 10 --min_af 0.65 --pplacer_cpus 1 --genome_dir bins --prefix SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi --out_dir SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi --cpus 30 --scratch_dir pplacer_tmp
  
  ================================================================================
                                       ERROR                                      
  ________________________________________________________________________________
  
             The GTDB-Tk reference data does not exist or is corrupted.           
  GTDBTK_DATA_PATH=gtdb/release202/202.0/auxillary_files/release202
  gtdb/release214/214.0/auxillary_files/gtdbtk_r214_data
  gtdb/release89/89.0/release89
  gtdb/release95/95.0/auxillary_files/release95
  
     Please compare the checksum to those provided in the download repository.    
            https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data          
  ================================================================================
  [2026-03-05 19:16:44] ERROR: Controlled exit resulting from early termination.

Command wrapper:
  ==========================================
  SLURM_JOB_ID = 2805636
  SLURM_JOB_NODELIST = b01-10
  TMPDIR = /tmp/SLURM_2805636
  ==========================================
  [2026-03-05 19:16:44] INFO: GTDB-Tk v2.5.2
  [2026-03-05 19:16:44] INFO: gtdbtk classify_wf --extension fa --min_perc_aa 10 --min_af 0.65 --pplacer_cpus 1 --genome_dir bins --prefix SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi --out_dir SPAdes-SemiBin2-unclassified-unrefined-CR180008_O_frankpressi --cpus 30 --scratch_dir pplacer_tmp
  
  ================================================================================
                                       ERROR                                      
  ________________________________________________________________________________
  
             The GTDB-Tk reference data does not exist or is corrupted.           
  GTDBTK_DATA_PATH=gtdb/release202/202.0/auxillary_files/release202
  gtdb/release214/214.0/auxillary_files/gtdbtk_r214_data
  gtdb/release89/89.0/release89
  gtdb/release95/95.0/auxillary_files/release95
  
     Please compare the checksum to those provided in the download repository.    
            https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data          
  ================================================================================
  [2026-03-05 19:16:44] ERROR: Controlled exit resulting from early termination.

Work dir:
  /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi/work/51/63a63cf8ffed925745b71587ba2606

Container:
  /project2/ckenkel_26/liruiqi/Osedax_meta/CR180008_Osedax_frankpressi/work/singularity/quay.io-biocontainers-gtdbtk-2.5.2--pyh1f0d9b5_0.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`