Process `detect:parse (1)` terminated with an error exit status (1) -- Error is ignored

SergeyBaikal commented 3 weeks ago

Dear authors, thank you for the program. I can't get it to run.

~/VIRify$ nextflow run EBI-Metagenomics/emg-viral-pipeline -r v0.4.0 --fasta "genome.fasta" --workdir /home/VIRify/work/ --databases /media/VIRify_DB/ --cores 8 -profile local,docker
N E X T F L O W  ~  version 22.10.7
Launching `https://github.com/EBI-Metagenomics/emg-viral-pipeline` [thirsty_gates] DSL2 - revision: f367002f0e [v0.4.0]

Profile: local,docker

Current User: ***
Nextflow-version: 22.10.7
Starting time: 18-02-2023 20:32 UTC
Workdir location:
  /home/VIRify/work
Databases location:
  /media/VIRify_DB/

Dev ViPhOG database: v3
Dev Meta database: v2

Only run annotation: false

[-        ] process > download_pprmeta:pprmetaGet    -
[-        ] process > download_virsorter_db:virso... -
[-        ] process > download_virfinder_db:virfi... -
[-        ] process > download_model_meta:metaGetDB  -
executor >  local (5)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [  0%] 0 of 1
[-        ] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [  0%] 0 of 1
[-        ] process > download_model_meta:metaGetDB  [  0%] 0 of 1
executor >  local (8)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [  0%] 0 of 1
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [  0%] 0 of 1
[cb/a3bd48] process > download_model_meta:metaGetDB  [  0%] 0 of 1
executor >  local (9)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [  0%] 0 of 1
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [  0%] 0 of 1
[cb/a3bd48] process > download_model_meta:metaGetDB  [  0%] 0 of 1
executor >  local (9)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [  0%] 0 of 1
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [  0%] 0 of 1
[cb/a3bd48] process > download_model_meta:metaGetDB  [  0%] 0 of 1
executor >  local (9)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [  0%] 0 of 1
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [  0%] 0 of 1
[cb/a3bd48] process > download_model_meta:metaGetDB  [100%] 1 of 1 ✔
executor >  local (9)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [100%] 1 of 1 ✔
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [  0%] 0 of 1
[cb/a3bd48] process > download_model_meta:metaGetDB  [100%] 1 of 1 ✔
executor >  local (9)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [100%] 1 of 1 ✔
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [100%] 1 of 1 ✔
[cb/a3bd48] process > download_model_meta:metaGetDB  [100%] 1 of 1 ✔
executor >  local (10)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [100%] 1 of 1 ✔
[e4/801559] process > download_virsorter_db:virso... [  0%] 0 of 1
[c8/30ca5c] process > download_virfinder_db:virfi... [100%] 1 of 1 ✔
[cb/a3bd48] process > download_model_meta:metaGetDB  [100%] 1 of 1 ✔
executor >  local (13)
[95/69c2c7] process > download_pprmeta:pprmetaGet    [100%] 1 of 1 ✔
[e4/801559] process > download_virsorter_db:virso... [100%] 1 of 1 ✔
[c8/30ca5c] process > download_virfinder_db:virfi... [100%] 1 of 1 ✔
[cb/a3bd48] process > download_model_meta:metaGetDB  [100%] 1 of 1 ✔
[46/0c0339] process > download_viphog_db:viphogGetDB [100%] 1 of 1 ✔
[5d/caa4a9] process > download_ncbi_db:ncbiGetDB     [100%] 1 of 1 ✔
[80/0d410b] process > download_checkv_db:checkvGetDB [100%] 1 of 1 ✔
[ed/2f7ad4] process > preprocess:rename (1)          [100%] 1 of 1 ✔
[02/5199b9] process > preprocess:length_filtering... [100%] 1 of 1 ✔
[86/cef90a] process > detect:virsorter (1)           [100%] 1 of 1 ✔
[97/546494] process > detect:virfinder (1)           [100%] 1 of 1 ✔
[d8/9cc9a7] process > detect:pprmeta (1)             [100%] 1 of 1 ✔
[f3/1ccf40] process > detect:parse (1)               [100%] 1 of 1, failed: 1 ✔
[-        ] process > postprocess:restore            -
[-        ] process > annotate:prodigal              -
[-        ] process > annotate:hmmscan_viphogs       -
[-        ] process > annotate:hmm_postprocessing    -
[-        ] process > annotate:ratio_evalue          -
[-        ] process > annotate:annotation            -
[-        ] process > annotate:plot_contig_map       -
[-        ] process > annotate:assign                -
[-        ] process > annotate:checkV                -
[-        ] process > plot:generate_krona_table      -
[-        ] process > plot:krona                     -
[-        ] process > plot:generate_sankey_table     -
[-        ] process > plot:sankey                    -
[f3/1ccf40] NOTE: Process `detect:parse (1)` terminated with an error exit status (1) -- Error is ignored
Completed at: 27-Sep-2024 12:18:24
Duration    : 1h 52m 10s
CPU hours   : 3.1 (0% failed)
Succeeded   : 12
Ignored     : 1
Failed      : 1

~/VIRify$

SergeyBaikal commented 3 weeks ago

I'm answering myself. If anyone else has the same problem. I input incorrect contigs. So check the run on the test contigs. emg-viral-pipeline-master/nextflow/test/assembly.fasta

mberacochea commented 3 weeks ago

Hi @SergeyBaikal,

Thank you for your feedback. The error message is indeed unhelpful, and we are actively working to improve the parameters validation and error handling to better address situations like this.

Cheers

EBI-Metagenomics / emg-viral-pipeline

Process `detect:parse (1)` terminated with an error exit status (1) -- Error is ignored #133