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GENERATE_CONFIG fails #131

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AlcaArctica opened this issue Dec 18, 2024 · 1 comment
Closed

GENERATE_CONFIG fails #131

AlcaArctica opened this issue Dec 18, 2024 · 1 comment
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@AlcaArctica
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AlcaArctica commented Dec 18, 2024 •
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Description of the bug

I am new to blobtoolkit, so this may be a user error. I successfully run the test, but struggle with my first own dataset. The pipeline fails at the very beginning when setting up the config. Here is the full output. Please kindly let me know how to fix this issue. Thank you very much!

(base) luelze@raven01:/ptmp/luelze/nextflow/nextflow_blobtoolkit> nextflow run sanger-tol/blobtoolkit -profile mpcdf,raven --input /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit/samplesheet.csv --outdir /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit --fasta /ptmp/luelze/analysis/wGorVio/hic/purge_dups/final/wgorvio_purged_plevel2_hap1.fasta --accession wGorVio --taxon 2597636 --taxdump /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/taxdump_2024_12 --blastp /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/uniprot_2024_12/reference_proteomes.dmnd --blastx /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/uniprot_2024_12/reference_proteomes.dmnd --blastn /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/nt_2024_12 --busco /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/busco_2024_12/v5/data/lineages --busco_lineages eukaryota_odb10 -r main

 N E X T F L O W   ~  version 24.10.3

Launching `https://github.com/sanger-tol/blobtoolkit` [high_goldberg] DSL2 - revision: 86ee868d71 [main]



------------------------------------------------------
   _____                                _______    _
  / ____|                              |__   __|  | |
 | (___   __ _ _ __   __ _  ___ _ __  ___ | | ___ | |
  \___ \ / _` | '_ \ / _` |/ _ \ '__||___|| |/ _ \| |
  ____) | (_| | | | | (_| |  __/ |        | | (_) | |____
 |_____/ \__,_|_| |_|\__, |\___|_|        |_|\___/|______|
                      __/ |
                     |___/
  sanger-tol/blobtoolkit v0.6.0-g86ee868
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : high_goldberg
  containerEngine           : singularity
  launchDir                 : /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit
  workDir                   : /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit/work
  projectDir                : /u/luelze/.nextflow/assets/sanger-tol/blobtoolkit
  userName                  : luelze
  profile                   : mpcdf,raven
  configFiles               : 

Input/output options
  input                     : /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit/samplesheet.csv
  busco_lineages            : eukaryota_odb10
  image_format              : png
  outdir                    : /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit

Reference genome options
  taxon                     : 2597636
  accession                 : wGorVio
  fasta                     : /ptmp/luelze/analysis/wGorVio/hic/purge_dups/final/wgorvio_purged_plevel2_hap1.fasta

Databases
  busco                     : /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/busco_2024_12/v5/data/lineages
  lineage_tax_ids           : /u/luelze/.nextflow/assets/sanger-tol/blobtoolkit/assets/mapping_taxids-busco_dataset_name.2019-12-16.txt
  blastp                    : /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/uniprot_2024_12/reference_proteomes.dmnd
  blastx                    : /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/uniprot_2024_12/reference_proteomes.dmnd
  blastn                    : /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/nt_2024_12
  taxdump                   : /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/taxdump_2024_12

Institutional config options
  config_profile_description: MPCDF raven profile (unofficially) provided by nf-core/configs.
  config_profile_contact    : James Fellows Yates (@jfy133)
  config_profile_url        : https://www.mpcdf.mpg.de/services/supercomputing

Max job request options
  max_cpus                  : 72
  max_memory                : 1.9 TB
  max_time                  : 1d

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use sanger-tol/blobtoolkit for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7949058

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/sanger-tol/blobtoolkit/blob/master/CITATIONS.md

executor >  slurm (3)
[ee/4b1d21] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMTOOLS_FLAGSTAT                   [  0%] 0 of 1
[97/852450] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)           [  0%] 0 of 1
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_INDEX                   -
[69/ba1536] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (wGorVio)           [  0%] 0 of 1
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:PIGZ_COMPRESS                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTK_DEPTH                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR               -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST                           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT                 -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY                        -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES                              -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR                -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                         -
ERROR ~ Error executing process > 'SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)'

Caused by:
  Process `SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)` terminated with an error exit status (1)
executor >  slurm (3)
[ee/4b1d21] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMTOOLS_FLAGSTAT                   [  0%] 0 of 1
[97/852450] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)           [100%] 1 of 1, failed: 1 ✘
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_INDEX                   -
[69/ba1536] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (wGorVio)           [  0%] 0 of 1
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:PIGZ_COMPRESS                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTK_DEPTH                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR               -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST                           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT                 -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY                        -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES                              -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR                -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                         -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)'

Caused by:
  Process `SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)` terminated with an error exit status (1)
executor >  slurm (4)
[ee/4b1d21] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[00/56d921] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMTOOLS_FLAGSTAT (wGorVio_T1)      [  0%] 0 of 1
[97/852450] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)           [100%] 1 of 1, failed: 1 ✘
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_INDEX                   -
[69/ba1536] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (wGorVio)           [  0%] 0 of 1
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:PIGZ_COMPRESS                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTK_DEPTH                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR               -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST                           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT                 -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY                        -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES                              -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR                -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                         -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)'

Caused by:
  Process `SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)` terminated with an error exit status (1)
executor >  slurm (4)
[ee/4b1d21] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[00/56d921] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMTOOLS_FLAGSTAT (wGorVio_T1)      [  0%] 0 of 1
[97/852450] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)           [100%] 1 of 1, failed: 1 ✘
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_INDEX                   -
[69/ba1536] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (wGorVio)           [100%] 1 of 1 ✔
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:PIGZ_COMPRESS                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTK_DEPTH                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR               -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST                           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT                 -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY                        -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES                              -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR                -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                         -

ERROR ~ Error executing process > 'SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)'

Caused by:
  Process `SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)` terminated with an error exit status (1)
executor >  slurm (4)
[ee/4b1d21] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[00/56d921] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMTOOLS_FLAGSTAT (wGorVio_T1)      [100%] 1 of 1 ✔
[97/852450] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)           [100%] 1 of 1, failed: 1 ✘
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_INDEX                   -
[69/ba1536] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (wGorVio)           [100%] 1 of 1 ✔
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:PIGZ_COMPRESS                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTK_DEPTH                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR               -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST                           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT                 -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY                        -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES                              -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR                -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                         -
-[sanger-tol/blobtoolkit] Pipeline completed with errors-
ERROR ~ Error executing process > 'SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)'

Caused by:
  Process `SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)` terminated with an error exit status (1)
executor >  slurm (4)
[ee/4b1d21] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[00/56d921] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMTOOLS_FLAGSTAT (wGorVio_T1)      [100%] 1 of 1 ✔
[97/852450] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)           [100%] 1 of 1, failed: 1 ✘
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_INDEX                   -
[69/ba1536] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (wGorVio)           [100%] 1 of 1 ✔
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:PIGZ_COMPRESS                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTK_DEPTH                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR               -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                       -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST                           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK                    -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN                         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT                 -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS           -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA                  -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY                        -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTK_IMAGES                              -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:BLOBTOOLKIT_UPDATEMETA         -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:FINALISE_BLOBDIR:COMPRESSBLOBDIR                -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC                                         -
-[sanger-tol/blobtoolkit] Pipeline completed with errors-
ERROR ~ Error executing process > 'SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)'

Caused by:
  Process `SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG (wGorVio)` terminated with an error exit status (1)


Command executed:

  generate_config.py \
      --fasta /ptmp/luelze/analysis/wGorVio/hic/purge_dups/final/wgorvio_purged_plevel2_hap1.fasta \
      --taxon_query "2597636" \
      --lineage_tax_ids mapping_taxids-busco_dataset_name.2019-12-16.txt \
      --busco 'eukaryota_odb10' \
      --accession wGorVio \
      --blastn nt_2024_12 \
      --yml_out wGorVio.yaml \
      --csv_out wGorVio.csv
  
  cat <<-END_VERSIONS > versions.yml
  "SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:GENERATE_CONFIG":
      generate_config.py: $(generate_config.py --version | cut -d' ' -f2)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    fuse2fs not found, will not be able to mount EXT3 filesystems
  Traceback (most recent call last):
    File "/u/luelze/.nextflow/assets/sanger-tol/blobtoolkit/bin/generate_config.py", line 266, in <module>
      sys.exit(main())
    File "/u/luelze/.nextflow/assets/sanger-tol/blobtoolkit/bin/generate_config.py", line 251, in main
      assembly_info = get_assembly_info(args.accession)
    File "/u/luelze/.nextflow/assets/sanger-tol/blobtoolkit/bin/generate_config.py", line 144, in get_assembly_info
      if response["total_count"] != 1:
  KeyError: 'total_count'

Work dir:
  /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit/work/97/852450cec4d43603a409a38f753da6

Container:
  /u/luelze/sw/nextflow/cache/docker.io-genomehubs-blobtoolkit-4.3.9.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`

 -- Check '.nextflow.log' file for details

Command used and terminal output

nextflow run sanger-tol/blobtoolkit -profile mpcdf,raven --input /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit/samplesheet.csv --outdir /raven/ptmp/luelze/nextflow/nextflow_blobtoolkit --fasta /ptmp/luelze/analysis/wGorVio/hic/purge_dups/final/wgorvio_purged_plevel2_hap1.fasta --accession wGorVio --taxon 2597636 --taxdump /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/taxdump_2024_12 --blastp /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/uniprot_2024_12/reference_proteomes.dmnd --blastx /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/uniprot_2024_12/reference_proteomes.dmnd --blastn /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/nt_2024_12 --busco /raven/ri/public_sequence_data/sanger-tol/blobtoolkit/busco_2024_12/v5/data/lineages --busco_lineages eukaryota_odb10 -r main

Relevant files

No response

System information

LSB Version: n/a
Distributor ID: SUSE
Description: SUSE Linux Enterprise Server 15 SP5
Release: 15.5
Codename: n/a
@AlcaArctica AlcaArctica added the bug Something isn't working label Dec 18, 2024
@AlcaArctica
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I figured out that leaving out --accession solves the problem.

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