Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked.

[alimalrashed]

Description of the bug

Hi everyone, I'm trying to add taxpasta parameters (e.g. --taxpasta_add_name, --taxpasta_add_rank) but I keep getting a command error exit status of 2 with the error being that a taxonomy is required. I asked on Slack and @jfy133 has suggested that it may be something to do with Taxonomy nodes/names dump files? Thanks!

Command used and terminal output

Command: 

nextflow run nf-core/taxprofiler -r 1.1.0 -profile docker --perform_shortread_qc --shortread_qc_tool fastp --shortread_qc_adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --shortread_qc_adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --perform_shortread_hostremoval --save_hostremoval_unmapped --shortread_hostremoval_index /data/Ali/databases/GRCh38_noalt_as_Phix --hostremoval_reference /data/Ali/databases/GRCh38_noalt_as_Phix/GCA_002596845.1_ASM259684v1_genomic.fna.gz --input /data/Ali/sample_lists/taxprofiler.s001script.D1.csv --databases /data/Ali/database_lists/taxprofiler.kraken2.centrifuge.krakenuniq.kaiju.csv --outdir /data/Ali/output/tax.2031.out --run_kraken2 --run_bracken --run_centrifuge --run_krakenuniq --run_profile_standardisation --run_krona --taxpasta_add_name --taxpasta_add_rank --taxpasta_add_lineage --taxpasta_add_idlineage --taxpasta_add_ranklineage

Error output:

[Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE (kraken2|kraken2db)'

Caused by:
  Process `NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE (kraken2|kraken2db)` terminated with an error exit status (2)

Command executed:

  taxpasta standardise \
      -p kraken2 -o kraken2_kraken2db.tsv --add-name --add-rank --add-lineage --add-id-lineage \
       \
      D1_se_D1_kraken2db.kraken2.kraken2.report.txt

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:STANDARDISATION_PROFILES:TAXPASTA_STANDARDISE":
      taxpasta: $(taxpasta --version)
  END_VERSIONS

Command exit status:
  2

Command output:
  [17:47:09] CRITICAL The '--add-name' option requires a        standardise.py:192
                      taxonomy. Please provide one using the                      
                      option '--taxonomy'.                                        

Command error:
  [17:47:09] CRITICAL The '--add-name' option requires a        standardise.py:192
                      taxonomy. Please provide one using the                      
                      option '--taxonomy'.

Relevant files

No response

System information

Taxprofiler version 1.1.0 Docker Linux

[jfy133]

Duplicate of #390