DEEPLC and MS2PIP doesnt work with multiple variable modifications

[yannic-chen]

Description of the bug

I have problems using MHCquant with multiple variable modifications.

The whole pipeline works when not specifying any modifciations. With multiple modifcations, the pipeline only works when not including DEEPLC and MS2PIP.

Command used and terminal output

sudo nextflow run nf-core/mhcquant --input 'samplesheet.tsv' --outdir OUTDIR_HLA1_PTM --fasta 'human_20365_conts_validated_conversion.fasta' --use_deeplc --use_ms2pip -profile docker -r 2.5.0 --digest_mass_range '500:2500' --activation_method CID --prec_charge '1:4' --fdr_threshold 0.01 --fdr_level psm_level_fdrs --number_mods 3 --precursor_mass_tolerance 15 --fragment_mass_tolerance 0.03 --num_hits 1 --peptide_min_length 7 --peptide_max_length 25 --variable_mods 'Oxidation (M),Acetyl (Protein N-term),Cysteinyl (C)'

-[nf-core/mhcquant] Pipeline completed with errors-                                                                                                                                                              ERROR ~ Error executing process > 'NFCORE_MHCQUANT:MHCQUANT:MS2PIP (4)'                                                                                                                                                                                                                                                                                                                                                           Caused by:                                                                                                                                                                                                         Process `NFCORE_MHCQUANT:MHCQUANT:MS2PIP (4)` terminated with an error exit status (1)                                                                                                                                                                                                                                                                                                                                          Command executed:                                                                                                                                                                                                                                                                                                                                                                                                                   ms2pip_cli.py \                                                                                                                                                                                                      --input_idxml G220824_010_Slot2-31_1_6735_deeplc.idXML \                                                                                                                                                         --input_mzml G220824_010_Slot2-31_1_6735.mzML \                                                                                                                                                                  --output_idxml G220824_010_Slot2-31_1_6735_deeplc_ms2pip.idXML \                                                                                                                                                 --num_hits 1 \                                                                                                                                                                                                   --model_name Immuno-HCD \                                                                                                                                                                                        --fragment_error 0.06 \                                                                                                                                                                                          --variable_mods 'Oxidation (M),Acetyl (Protein N-term),Cysteinyl (C)' \
      --fixed_mods ' ' \
      --num_cpus 2

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MHCQUANT:MHCQUANT:MS2PIP":
      MS2PIP: $(conda list | grep "ms2pip" | awk 'NR==2 {print $2}')
  END_VERSIONS

Command exit status:
  1

Command output:
  Warning: OPENMS_DATA_PATH environment variable not found and no share directory was installed. Some functionality might not work as expected.

Command error:
  2023-12-14 09:44:18,068 - MS2pip prediction - INFO - Parse idXML
  2023-12-14 09:44:26,276 - MS2pip prediction - INFO - Generate params file for MS2pip
  2023-12-14 09:44:26,277 - MS2pip prediction - INFO - Make MS2pip predictions                                                                                                                                     Warning: OPENMS_DATA_PATH environment variable not found and no share directory was installed. Some functionality might not work as expected.
  Traceback (most recent call last):
    File "/root/.nextflow/assets/nf-core/mhcquant/bin/ms2pip_cli.py", line 247, in <module>                                                                                                                            sys.exit(main())
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__                                                                                                                               return self.main(*args, **kwargs)
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main                                                                                                                                   rv = self.invoke(ctx)
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke                                                                                                                                 return ctx.invoke(self.callback, **ctx.params)
    File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke                                                                                                                                  return __callback(*args, **kwargs)
    File "/root/.nextflow/assets/nf-core/mhcquant/bin/ms2pip_cli.py", line 215, in main                                                                                                                                ms2pip = MS2PIP(pep_file=df_peprec, spec_file=input_mzml, params=params, return_results=True, num_cpu=num_cpus)                                                                                                File "/usr/local/lib/python3.10/site-packages/ms2pip/ms2pipC.py", line 765, in __init__                                                                                                                            self.mods.add_from_ms2pip_modstrings(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/peptides.py", line 107, in add_from_ms2pip_modstrings                                                                                                         raise InvalidAminoAcidError(amino_acid)
  ms2pip.exceptions.InvalidAminoAcidError: X

Work dir:
  /home/chyannic/YC/test_mhcquant/work/4d/1c4c1514c0446aa69019d8901235a2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

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

Relevant files

nextflow.log

System information

Freshly installed everything last week, so should be the newest version