Taxpasta parameters produce an error exit status of 2 during standardise part

[AndreaQ7]

Description of the bug

Hello everyone,
I am getting the following error during the taxpasta standardise function using the data from the tutorial age:

Execution cancelled -- Finishing pending tasks before exit
-[nf-core/taxprofiler] Pipeline completed with errors-
[84/f9989c] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:KRAKENTOOLS_COMBINEKREPORTS_C
ENTRIFUGE (2)` terminated with an error exit status (1) -- Error is ignored
[fd/db45c6] NOTE: Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:KRAKENTOOLS_COMBINEKREPORTS_C
ENTRIFUGE (1)` terminated with an error exit status (1) -- Error is ignored
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE 
(kaiju|db3)'

Caused by:
  Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE (kaiju|db3)` terminated 
with an error exit status (2)


Command executed:

  taxpasta standardise \
       \
       \
      ERX5474932_pe_db3.kaijutable.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE":
      taxpasta: $(taxpasta --version)
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Usage: taxpasta standardise [OPTIONS] PROFILE
  Try 'taxpasta standardise -h' for help.
  ╭─ Error ─────────────────────────────────────────────────────────────────────────────────────────────────────
─╮
  │ Missing option '--profiler' / '-p'. Choose from:                                                            
 │
  │         bracken,                                                                                            
 │
  │         centrifuge,                                                                                         
 │
  │         diamond,                                                                                            
 │
  │         ganon,                                                                                              
 │
  │         kaiju,                                                                                              
 │
  │         kmcp,                                                                                               
 │
  │         kraken2,                                                                                            
 │
  │         krakenuniq,                                                                                         
 │
  │         megan6,                                                                                             
 │
  │         metaphlan,                                                                                          
 │
  │         motus                                                                                               
 │
  ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────
─╯

[Midnighter]

It looks like the kaiju profiler option is not set, for some reason...

[Midnighter]

@AndreaQ7 can you please provide the command that you used to start the pipeline and your database file?

[AndreaQ7]

Yes of course, I followed the tutorial: https://nf-co.re/taxprofiler/1.1.8/docs/usage/usage/tutorials/d
So the databases are the ones called "test-db-centrifuge.tar.gz" and "test-db-kraken2.tar.gz" and the command line is the one reported in the tutorial

nextflow run nf-core/taxprofiler -r 1.1.0 -profile conda\
--input samplesheet.csv --databases database.csv --outdir ./results \
--perform_shortread_qc \
--perform_shortread_hostremoval --hostremoval_reference GCF_000819615.1_ViralProj14015_genomic.fna.gz \
--perform_runmerging --save_runmerged_reads \
--run_centrifuge --run_kaiju --run_kraken2 \
--run_profile_standardisation \
--max_cpus 2 --max_memory '6.GB'

[Midnighter]

I just ran the exact same command with the preparatory steps from the tutorial and it completes successfully... So I cannot reproduce your error. Can you please try again from the start? You could also run the latest version -r 1.1.8.

[jfy133]

I agree @AndreaQ7 please try with the most recent version of the pipeline. 1.1.0 is very old comparatively :D