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nf-core / mhcquant

Identify and quantify MHC eluted peptides from mass spectrometry raw data
https://nf-co.re/mhcquant
MIT License
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DEEPLC and MS2PIP doesnt work with multiple variable modifications #294

Closed yannic-chen closed 5 months ago

yannic-chen commented 11 months ago

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

jonasscheid commented 11 months ago

Hi @yannic-chen! Thanks for reporting this issue. I could also reproduce it locally with a small testset. That reminds me of including tests for multiple variable or fixed modifications.

There won't be a fix for the deeplc and ms2pip scripts in the next release, since we want to use MS2Rescore to handle all kinds of configurations. So I just merged a PR that removed the deeplc and ms2pip modules, and implemented an ms2rescore module. Could you try using the dev branch with -r dev? That worked for me. So I'll give you a quick outline how to use it :

You can call e.g. ms2pip and deeplc via a new cli flag --feature_generators deeplc,ms2pip,... no need for use_deeplc and use_ms2pip anymore. Further feature generators you can read up in the ms2rescore doc.

If you only want psm_level_fdr then you can also specify a new cli flag --rescoring_engine mokapot instead of percolator (default), to get a handy ms2rescore report in the multiqc folder. peptide_level_fdrs are currently only applicable with percolator, since ms2rescore+mokapot currently only reports psm-level-fdr estimates.

Let me know if that works for you as well!

yannic-chen commented 10 months ago

Hi @jonasscheid, Thank you for the quick reply. I have followed your instruction, which led me to the following error:

Pipeline completed with errors
~ Error executing process > 'NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (WT_A)'
Caused by:
Process NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (WT_A) terminated with an error exit status (1)
Command executed:
ms2rescore_cli.py \
--psm_file WT_A.idXML \
--spectrum_path . \
--output_path WT_A_ms2rescore.idXML \
--processes 12 \
--ms2_tolerance 0.06 --ms2pip_model Immuno-HCD --rescoring_engine mokapot --feature_generators deeplc,ms2pip
cat <<-END_VERSIONS > versions.yml
"NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE":
MS²Rescore: $(echo $(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \(v\K[^\)]+' ))
END_VERSIONS
Command exit status:
1
Command output:    

Command error:
  2024-01-16 13:21:13,284 WARNING Could not add the following atom: Se
  2024-01-16 13:21:13,289 WARNING Skipping the following (not in library): 4 ('U', None)
  2024-01-16 13:21:13,335 WARNING Could not add the following value: pos 1 for atom Se with value 1
  2024-01-16 13:21:13,335 WARNING Could not add the following atom: Se
  2024-01-16 13:21:13,335 WARNING Skipping the following (not in library): 1 ('U', None)
  2024-01-16 13:21:20,487 WARNING Could not add the following value: pos 4 for atom Se with value 1
  2024-01-16 13:21:20,487 WARNING Could not add the following atom: Se
  2024-01-16 13:21:20,491 WARNING Skipping the following (not in library): 4 ('U', None)
  2024-01-16 13:21:32,355 WARNING Could not add the following value: pos 4 for atom Se with value 1
  2024-01-16 13:21:32,355 WARNING Could not add the following atom: Se
  2024-01-16 13:21:32,355 WARNING Skipping the following (not in library): 4 ('U', None)
  2024-01-16 13:24:14,538 WARNING Removed 105 PSMs that were missing one or more rescoring feature(s), {'abs_diff_Q1_norm', 'iony_abs_diff_Q1', 'ionb_spearman', 'dotprod_ionb_norm', 'spec_pearson', 'iony_min_abs_diff_norm', 'spec_pearson_norm', 'dotprod_iony', 'ionb_max_abs_diff_norm', 'ionb_abs_diff_Q3_norm', 'ionb_abs_diff_Q1', 'iony_mean_abs_diff_norm', 'iony_mse', 'spec_spearman', 'iony_max_abs_diff_norm', 'iony_abs_diff_Q2', 'min_abs_diff', 'ionb_pearson_norm', 'ionb_abs_diff_Q1_norm', 'ionb_mse_norm', 'iony_abs_diff_Q3_norm', 'spec_mse_norm', 'ionb_mean_abs_diff', 'dotprod_ionb', 'iony_abs_diff_Q3', 'cos_iony', 'cos_norm', 'mean_abs_diff_norm', 'min_abs_diff_iontype', 'min_abs_diff_norm', 'ionb_min_abs_diff_norm', 'ionb_abs_diff_Q2', 'cos', 'abs_diff_Q3_norm', 'abs_diff_Q1', 'iony_std_abs_diff', 'ionb_mean_abs_diff_norm', 'iony_spearman', 'cos_iony_norm', 'ionb_abs_diff_Q2_norm', 'iony_std_abs_diff_norm', 'cos_ionb', 'ionb_abs_diff_Q3', 'spec_mse', 'std_abs_diff', 'ionb_std_abs_diff', 'ionb_mse', 'abs_diff_Q3', 'max_abs_diff_iontype', 'iony_mean_abs_diff', 'max_abs_diff_norm', 'iony_pearson_norm', 'iony_min_abs_diff', 'ionb_pearson', 'abs_diff_Q2', 'mean_abs_diff', 'ionb_max_abs_diff', 'dotprod', 'dotprod_norm', 'iony_pearson', 'abs_diff_Q2_norm', 'iony_abs_diff_Q2_norm', 'cos_ionb_norm', 'max_abs_diff', 'std_abs_diff_norm', 'iony_mse_norm', 'iony_abs_diff_Q1_norm', 'ionb_std_abs_diff_norm', 'dotprod_iony_norm', 'ionb_min_abs_diff', 'iony_max_abs_diff'}.
  2024-01-16 13:34:38,542 INFO Identified 99077 (187.10%) more PSMs at 1% FDR after rescoring.
  2024-01-16 13:34:38,542 INFO Writing output to WT_A_ms2rescore.idXML.psms.tsv...
  2024-01-16 13:36:12,847 INFO Collecting files...
  2024-01-16 13:36:12,847 INFO ✅ Found PSMs: 'WT_A_ms2rescore.idXML.psms.tsv'
  2024-01-16 13:36:12,847 INFO ✅ Found configuration: 'WT_A_ms2rescore.idXML.full-config.json'
  2024-01-16 13:36:12,847 INFO ✅ Found feature names: 'WT_A_ms2rescore.idXML.feature_names.tsv'
  2024-01-16 13:36:12,848 INFO ✅ Found feature weights: 'WT_A_ms2rescore.idXML.mokapot.weights.tsv'
  2024-01-16 13:36:12,848 WARNING ❌ log: 'WT_A_ms2rescore.idXML.log.txt'
  2024-01-16 13:36:12,848 INFO Recalculating confidence estimates...
  Traceback (most recent call last):
    File "/root/.nextflow/assets/nf-core/mhcquant/bin/ms2rescore_cli.py", line 175, 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/ms2rescore_cli.py", line 171, in main
      rescore_idxml(kwargs["psm_file"], kwargs["output_path"], config)
    File "/root/.nextflow/assets/nf-core/mhcquant/bin/ms2rescore_cli.py", line 81, in rescore_idxml
      rescore(config, psm_list)
    File "/usr/local/lib/python3.10/site-packages/ms2rescore/core.py", line 151, in rescore
      generate.generate_report(
    File "/usr/local/lib/python3.10/site-packages/ms2rescore/report/generate.py", line 87, in generate_report
      confidence_before, confidence_after = get_confidence_estimates(psm_list, fasta_file)              
    File "/usr/local/lib/python3.10/site-packages/ms2rescore/report/utils.py", line 40, in get_confidence_estimates
      score_before = pd.DataFrame.from_records(psm_list["provenance_data"])[
    File "/usr/local/lib/python3.10/site-packages/pandas/core/frame.py", line 2335, in from_records
      arrays, columns = to_arrays(data, columns)
    File "/usr/local/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 867, in to_arrays
      arr, columns = _list_of_dict_to_arrays(data, columns)
    File "/usr/local/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 954, in _list_of_dict_to_arrays
      content = lib.dicts_to_array(data, list(columns))
    File "pandas/_libs/lib.pyx", line 447, in pandas._libs.lib.dicts_to_array
  numpy.core._exceptions._ArrayMemoryError: Unable to allocate 4.42 TiB for an array with shape (964370, 629314) and data type object

Work dir:
  /home/chyannic/YC/test_mhcquant/work/02/34682d0057994344f573816d3feed8

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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

I used the following command: sudo nextflow run nf-core/mhcquant --input samplesheet_HLA1.tsv --outdir OUTDIR_HLA1_PTM_featureGenerators --fasta human_20365_conts_validated_conversion.fasta -profile docker -r dev --feature_generators deeplc,ms2pip --rescoring_engine mokapot --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)' -resume

The --feature_generators for ms2pip is by default "ms2pip": {"model": "HCD", "ms2_tolerance": 0.02}. How could I change the model to, for example "CID"?

Thank you for the good work.

jonasscheid commented 10 months ago

Unable to allocate 4.42 TiB for an array with shape (964370, 629314) and data type object

That is a big input file you have right there! Looks like you ran out of memory. By default the MS2RESCORE module uses process_high, see specs here. Thats sufficient for most requests. If you need to allocate more, you can provide a custom config file that can be given via -c <name>.config containing e.g.

process { withName: 'MS2RESCORE'{ memory = 5500.GB } }

Fingers crossed that your setup has these specs

The --feature_generators for ms2pip is by default "ms2pip": {"model": "HCD", "ms2_tolerance": 0.02}. How could I change the model to, for example "CID"?

That is default ms2rescore, but in mhcquant the default is overwritten to Immuno-HCD, see your error message:

--ms2_tolerance 0.06 --ms2pip_model Immuno-HCD --rescoring_engine mokapot --feature_generators deeplc,ms2pip

You can use the model names of ms2pip documented on their github repo

Let me know if that helped. You can also use our Slack channel if you want to discuss in more depth.

yannic-chen commented 10 months ago

Thanks for the quick response.

The input were 12 files which are less than 40GB in total.

I have redone the analysis now with only 2 input files, which now gives me another error.

executor >  local (8)                                                                                                                                                                                            [3d/1a427d] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_HLA1_single.tsv)   [100%] 1 of 1 ✔                                                                                     [33/ebe7a0] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (human_20365_conts_validated_conversion) [100%] 1 of 1 ✔                                                                                     [-        ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER                                           -                                                                                                   [ff/7ea3d6] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML (1)                                                  [100%] 2 of 2, cached: 2 ✔                                                                          [a5/fa2671] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (2)                                       [100%] 2 of 2 ✔                                                                                     [7d/58b0df] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_PEPTIDEINDEXER (2)                                     [100%] 2 of 2 ✔                                                                                     [c7/3b6599] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDMERGER (WT_A)                                        [100%] 1 of 1 ✔                                                                                     [43/3d8aab] process > NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (WT_A)                                             [100%] 1 of 1, failed: 1 ✘                                                                          [-        ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDSCORESWITCHER                                        -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDFILTER_Q_VALUE                                       -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:OPENMS_IDRIPPER                                         -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:PYOPENMS_IDFILTER                                       -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:MAP_ALIGNMENT:OPENMS_MAPALIGNERIDENTIFICATION           -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:MAP_ALIGNMENT:OPENMS_MAPRTTRANSFORMERMZML               -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:MAP_ALIGNMENT:OPENMS_MAPRTTRANSFORMERIDXML              -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:OPENMS_IDMERGER_QUANT                                   -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:PROCESS_FEATURE:OPENMS_FEATUREFINDERIDENTIFICATION      -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:PROCESS_FEATURE:OPENMS_FEATURELINKERUNLABELEDKD         -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:QUANT:PROCESS_FEATURE:OPENMS_IDCONFLICTRESOLVER               -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_TEXTEXPORTER                                           -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_MZTABEXPORTER                                          -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:CUSTOM_DUMPSOFTWAREVERSIONS                                   -                                                                                                   [-        ] process > NFCORE_MHCQUANT:MHCQUANT:MULTIQC                                                       -                                                                                                   Execution cancelled -- Finishing pending tasks before exit
-[nf-core/mhcquant] Pipeline completed with errors-                                                                                                                                                              ERROR ~ Error executing process > 'NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (WT_A)'                                                                                                                                                                                                                                                                                                                                                    Caused by:                                                                                                                                                                                                         Process `NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (WT_A)` terminated with an error exit status (1)                                                                                                                                                                                                                                                                                                                                   Command executed:                                                                                                                                                                                                                                                                                                                                                                                                                   ms2rescore_cli.py \                                                                                                                                                                                                  --psm_file WT_A.idXML \                                                                                                                                                                                          --spectrum_path . \                                                                                                                                                                                              --output_path WT_A_ms2rescore.idXML \                                                                                                                                                                            --processes 12 \                                                                                                                                                                                                 --ms2_tolerance 0.06 --ms2pip_model CID --rescoring_engine mokapot --feature_generators deeplc,ms2pip                                                                                                                                                                                                                                                                                                                         cat <<-END_VERSIONS > versions.yml                                                                                                                                                                               "NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE":                                                                                                                                                                               MS²Rescore: $(echo $(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \(v\K[^\)]+' ))                                                                                                                       END_VERSIONS                                                                                                                                                                                                                                                                                                                                                                                                                    Command exit status:                                                                                                                                                                                               1                                                                                                                                                                                                                                                                                                                                                                                                                               Command output:                                                                                                                                                                                                    (empty)                                                                                                                                                                                                                                                                                                                                                                                                                         Command error:                                                                                                                                                                                                         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/ms2rescore_cli.py", line 171, in main                                                                                                                            rescore_idxml(kwargs["psm_file"], kwargs["output_path"], config)                                                                                                                                               File "/root/.nextflow/assets/nf-core/mhcquant/bin/ms2rescore_cli.py", line 81, in rescore_idxml 
      rescore(config, psm_list)                                                                                                                                                                          [0/1626]    File "/usr/local/lib/python3.10/site-packages/ms2rescore/core.py", line 76, in rescore
      fgen.add_features(psm_list)
    File "/usr/local/lib/python3.10/site-packages/ms2rescore/feature_generators/ms2pip.py", line 190, in add_features
      ms2pip_results = correlate(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/core.py", line 178, in correlate
      ms2pip_parallelized = _Parallelized(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/core.py", line 331, in __init__
      validate_requested_xgb_model(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/_utils/xgb_models.py", line 21, in validate_requested_xgb_model
      _download_model(model_file, xgboost_model_hashes[model_file], model_dir)
    File "/usr/local/lib/python3.10/site-packages/ms2pip/_utils/xgb_models.py", line 98, in _download_model
      urllib.request.urlretrieve(
    File "/usr/local/lib/python3.10/urllib/request.py", line 241, in urlretrieve
      with contextlib.closing(urlopen(url, data)) as fp:
    File "/usr/local/lib/python3.10/urllib/request.py", line 216, in urlopen
      return opener.open(url, data, timeout)
    File "/usr/local/lib/python3.10/urllib/request.py", line 525, in open
      response = meth(req, response)
    File "/usr/local/lib/python3.10/urllib/request.py", line 634, in http_response
      response = self.parent.error(
    File "/usr/local/lib/python3.10/urllib/request.py", line 557, in error
      rescore(config, psm_list)                                                                                                                                                                          [0/1626]    File "/usr/local/lib/python3.10/site-packages/ms2rescore/core.py", line 76, in rescore
      fgen.add_features(psm_list)
    File "/usr/local/lib/python3.10/site-packages/ms2rescore/feature_generators/ms2pip.py", line 190, in add_features
      ms2pip_results = correlate(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/core.py", line 178, in correlate
      ms2pip_parallelized = _Parallelized(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/core.py", line 331, in __init__
      validate_requested_xgb_model(
    File "/usr/local/lib/python3.10/site-packages/ms2pip/_utils/xgb_models.py", line 21, in validate_requested_xgb_model
      _download_model(model_file, xgboost_model_hashes[model_file], model_dir)
    File "/usr/local/lib/python3.10/site-packages/ms2pip/_utils/xgb_models.py", line 98, in _download_model
      urllib.request.urlretrieve(
    File "/usr/local/lib/python3.10/urllib/request.py", line 241, in urlretrieve
      with contextlib.closing(urlopen(url, data)) as fp:
    File "/usr/local/lib/python3.10/urllib/request.py", line 216, in urlopen
      return opener.open(url, data, timeout)
    File "/usr/local/lib/python3.10/urllib/request.py", line 525, in open
      response = meth(req, response)
    File "/usr/local/lib/python3.10/urllib/request.py", line 634, in http_response
      response = self.parent.error(
    File "/usr/local/lib/python3.10/urllib/request.py", line 557, in error
      result = self._call_chain(*args)
    File "/usr/local/lib/python3.10/urllib/request.py", line 496, in _call_chain
      result = func(*args)                                                                                                                                                                                           File "/usr/local/lib/python3.10/urllib/request.py", line 749, in http_error_302
      return self.parent.open(new, timeout=req.timeout)
    File "/usr/local/lib/python3.10/urllib/request.py", line 525, in open
      response = meth(req, response)                                                                                                                                                                                 File "/usr/local/lib/python3.10/urllib/request.py", line 634, in http_response
      response = self.parent.error(
    File "/usr/local/lib/python3.10/urllib/request.py", line 563, in error
      return self._call_chain(*args)
    File "/usr/local/lib/python3.10/urllib/request.py", line 496, in _call_chain
      result = func(*args)
    File "/usr/local/lib/python3.10/urllib/request.py", line 643, in http_error_default
      raise HTTPError(req.full_url, code, msg, hdrs, fp)
  urllib.error.HTTPError: HTTP Error 403: Forbidden

Work dir:
  /home/chyannic/YC/test_mhcquant/work/43/3d8aab086da85dc731af723bc436e3

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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

Is it expected to require around 100x the total filesize in RAM for ms2rescore?

PS: it seems like the Slack channel you linked require specific e-mail address extension to work.

jonasscheid commented 10 months ago

urllib.error.HTTPError: HTTP Error 403: Forbidden

Do you run offline?

Is it expected to require around 100x the total filesize in RAM for ms2rescore?

Normally not. Do you mind sharing your little test dataset such that I can run some tests on it? is

PS: Apologies, maybe that one helps https://nf-co.re/join

EDIT: Can reproduce your error. Is a docker-related issue. I'll update you as soon as I have a fix

jonasscheid commented 7 months ago

Fixed in the 2.6.0dev version by #302