bigbio / bigbio/quantms

Chymotrypsin/P force in ComentAdapter, not supported by OpenMS

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#465 1 comment 0 reactions 2 assignees Claimed by @timosachsenberg View on GitHub
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Description

### Description of the bug

@timosachsenberg I thought this PR https://github.com/OpenMS/OpenMS/pull/7714 added `Chymotrypsin/P` in OpenMS.

```
The exit status of the task that caused the workflow execution to fail was: 6

Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3)'

Caused by:
Process `NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET (20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3)` terminated with an error exit status (6)

Command executed:

CometAdapter \
-in 20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3.mzML \
-out 20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3_comet.idXML \
-threads 8 \
-database "Homo-sapiens-uniprot-reviewed-contam-entrap-decoy-20241105.fasta" \
-instrument high_res \
-missed_cleavages 2 \
-min_peptide_length 6 \
-max_peptide_length 40 \
-num_hits 1 \
-num_enzyme_termini fully \
-enzyme "Chymotrypsin/P" \
-isotope_error 0/1 \
-precursor_charge 2:4 \
-fixed_modifications 'Carbamidomethyl (C)' \
-variable_modifications 'Acetyl (Protein N-term)' 'Deamidated (N)' 'Deamidated (Q)' 'Glu->pyro-Glu (N-term E)' 'Gln->pyro-Glu (N-term Q)' 'Oxidation (M)' 'Phospho (S)' 'Phospho (T)' 'Phospho (Y)' \
-max_variable_mods_in_peptide 3 \
-precursor_mass_tolerance 10.0 \
-precursor_error_units ppm \
-fragment_mass_tolerance 0.015 \
-fragment_bin_offset 0.0 \
-minimum_peaks 10 \
-PeptideIndexing:IL_equivalent \
-PeptideIndexing:unmatched_action warn \
-debug 0 \
-force \
\
2>&1 | tee 20150708_QE3_UPLC8_DBJ_QC_HELA_39frac_Chymotrypsin_3_comet.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET":
CometAdapter: $(CometAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
Comet: $(comet 2>&1 | grep -E "Comet version.*" | sed 's/ Comet version //g' | sed 's/"//g')
END_VERSIONS

Command exit status:
6

Command output:
Invalid string parameter value 'Chymotrypsin/P' for parameter 'enzyme' given! Valid values are: 'Lys-C,Lys-N,Chymotrypsin,CNBr,unspecific cleavage,Arg-C/P,Asp-N,Trypsin,Arg-C,Lys-C/P,PepsinA,Trypsin/P,leukocyte elastase,glutamyl endopeptidase,no cleavage'. Updating failed!
Parameters passed to 'CometAdapter' are invalid. To prevent usage of wrong defaults, please update/fix the parameters!

Command wrapper:
Invalid string parameter value 'Chymotrypsin/P' for parameter 'enzyme' given! Valid values are: 'Lys-C,Lys-N,Chymotrypsin,CNBr,unspecific cleavage,Arg-C/P,Asp-N,Trypsin,Arg-C,Lys-C/P,PepsinA,Trypsin/P,leukocyte elastase,glutamyl endopeptidase,no cleavage'. Updating failed!
Parameters passed to 'CometAdapter' are invalid. To prevent usage of wrong defaults, please update/fix the parameters!

Work dir:
/hps/nobackup/juan/pride/reanalysis/absolute-expression/cell-lines/PXD004452/work/9e/50c7621adb58fce5f479b4aec26a1b

Container:
/hps/nobackup/juan/pride/reanalysis/singularity/ghcr.io-openms-openms-tools-thirdparty-sif-latest.img

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

### Command used and terminal output

_No response_

### Relevant files

_No response_

### System information

_No response_

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