Error ms2rescore in big dataset for one run.

[ypriverol]

Description of the bug

This command is failing:

#!/usr/bin/env bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.

quantmsutilsc ms2rescore \
    --psm_file f07531_Prot_02_R2_F08_msgf.idXML \
    --spectrum_path . \
    --ms2_tolerance 0.4 \
    --output_path f07531_Prot_02_R2_F08_msgf_ms2rescore.idXML \
    --ms2pip_model_dir null \
    --processes 372 \
    --id_decoy_pattern ^DECOY_ \
    --ms2pip_model TMT --rescoring_engine percolator --calibration_set_size 0.15 --test_fdr 0.05 --feature_generators deeplc,ms2pip \
    2>&1 | tee f07531_Prot_02_R2_F08_ms2rescore.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:MS2RESCORE":
    MS2Rescore: $(echo $(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \(v\K[^\)]+' )
END_VERSIONS

Error here:

Error: 2024-11-25 15:33:11,160 [<module>] - Creating converter from 7 to 5
2024-11-25 15:33:11,160 [<module>] - Creating converter from 5 to 7
2024-11-25 15:33:11,160 [<module>] - Creating converter from 7 to 5
2024-11-25 15:33:11,160 [<module>] - Creating converter from 5 to 7
2024-11-25 15:33:11,207 [register_filter] - Registered filter: bshuf (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5bshuf.so)
2024-11-25 15:33:11,210 [register_filter] - Registered filter: blosc (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5blosc.so)
2024-11-25 15:33:11,212 [register_filter] - Registered filter: blosc2 (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5blosc2.so)
2024-11-25 15:33:11,213 [register_filter] - Registered filter: bzip2 (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5bzip2.so)
2024-11-25 15:33:11,216 [register_filter] - Registered filter: fcidecomp (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5fcidecomp.so)
2024-11-25 15:33:11,217 [register_filter] - Registered filter: lz4 (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5lz4.so)
2024-11-25 15:33:11,220 [register_filter] - Registered filter: sz (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5sz.so)
2024-11-25 15:33:11,232 [register_filter] - Registered filter: sz3 (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5sz3.so)
2024-11-25 15:33:11,233 [register_filter] - Registered filter: zfp (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5zfp.so)
2024-11-25 15:33:11,234 [register_filter] - init_filter not found for filter zstd: Init phase skipped.
2024-11-25 15:33:11,234 [register_filter] - Registered filter: zstd (/usr/local/lib/python3.10/site-packages/hdf5plugin/plugins/libh5zstd.so)
2024-11-25 15:33:12,843 [<module>] - Falling back to TensorFlow client; we recommended you install the Cloud TPU client directly with pip install cloud-tpu-client.
2024-11-25 15:33:15,677 [wrapper] - matplotlib data path: /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data
2024-11-25 15:33:15,683 [wrapper] - CONFIGDIR=/homes/pst_prd/.config/matplotlib
2024-11-25 15:33:15,684 [<module>] - interactive is False
2024-11-25 15:33:15,684 [<module>] - platform is linux
2024-11-25 15:33:15,815 [wrapper] - CACHEDIR=/homes/pst_prd/.cache/matplotlib
2024-11-25 15:33:15,817 [_load_fontmanager] - Using fontManager instance from /homes/pst_prd/.cache/matplotlib/fontlist-v390.json
2024-11-25 15:33:16,706 [parse_cli_arguments_to_config] - Percolator rescoring engine has been specified. Use the idXML containing rescoring features and run Percolator in a separate step.
2024-11-25 15:33:16,706 [ms2rescore] - MS²Rescore config:
2024-11-25 15:33:16,706 [ms2rescore] - {'$schema': './config_schema.json', 'ms2rescore': {'feature_generators': {'ms2pip': {'model_dir': 'null', 'model': 'TMT', 'ms2_tolerance': 0.4}, 'deeplc': {'deeplc_retrain': False, 'calibration_set_size': 0.15}}, 'rescoring_engine': {}, 'co
nfig_file': None, 'psm_file': None, 'psm_file_type': 'infer', 'psm_reader_kwargs': {}, 'spectrum_path': '.', 'output_path': 'f07531_Prot_02_R2_F08_msgf_ms2rescore.idXML', 'log_level': 'info', 'id_decoy_pattern': '^DECOY_', 'psm_id_pattern': '(.*)', 'spectrum_id_pattern': '(.*)',
 'lower_score_is_better': True, 'modification_mapping': {}, 'fixed_modifications': {}, 'processes': 48, 'rename_to_usi': False, 'fasta_file': None, 'write_report': True, 'ms2pip_model_dir': 'null', 'ms2pip_model': 'TMT', 'ms2_tolerance': 0.4, 'calibration_set_size': 0.15, 'rng':
 4711}}
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 "/usr/local/bin/quantmsutilsc", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/quantmsutils/quantmsutilsc.py", line 38, in main
    cli()
  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 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_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 "/usr/local/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/quantmsutils/rescoring/ms2rescore.py", line 375, in ms2rescore
    rescore_idxml(psm_file, output_path, config)
  File "/usr/local/lib/python3.10/site-packages/quantmsutils/rescoring/ms2rescore.py", line 123, in rescore_idxml
    psm_list = reader.read_file()
  File "/usr/local/lib/python3.10/site-packages/psm_utils/io/_base_classes.py", line 46, in read_file
    return PSMList(psm_list=[psm for psm in self.__iter__()])
  File "/usr/local/lib/python3.10/site-packages/psm_utils/io/_base_classes.py", line 46, in <listcomp>
    return PSMList(psm_list=[psm for psm in self.__iter__()])
  File "/usr/local/lib/python3.10/site-packages/psm_utils/io/idxml.py", line 112, in __iter__
    yield self._parse_psm(self.protein_ids, peptide_id, peptide_hit)
  File "/usr/local/lib/python3.10/site-packages/psm_utils/io/idxml.py", line 201, in _parse_psm
    rescoring_features={
  File "/usr/local/lib/python3.10/site-packages/psm_utils/io/idxml.py", line 202, in <dictcomp>
    key: float(peptide_hit.getMetaValue(key)) for key in self.rescoring_features
TypeError: float() argument must be a string or a real number, not 'NoneType'

Command used and terminal output

No response

Relevant files

Dataset here: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/94508cae253c72810c2dc0200e2c3e/

System information

No response