processing mascot results throws error in "processing scan file 0" stage

[martinPasen]

error message:

2022-11-03 16:34:51.227727: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: CUDA_ERROR_UNKNOWN: unknown error Models already downloaded. Formatted Prosit input written. 2/2 [==============================] - 2s 185ms/step 2/2 [==============================] - 3s 310ms/step MS Search Results ready. Basic Features added, adding Spectral Features. Processing scan file 0. Traceback (most recent call last): File "/home/martin.pasen/Code/prosit-library-reanalises/run_inspire.py", line 56, in run_inspire(config_path) File "/home/martin.pasen/Code/prosit-library-reanalises/run_inspire.py", line 47, in run_inspire create_features(config) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/inspire/feature_creation.py", line 603, in create_features write_rescoring_features( File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/inspire/feature_creation.py", line 514, in write_rescoring_features write_with_spectral_features( File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/inspire/feature_creation.py", line 227, in write_with_spectral_features process_single_file( File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/inspire/feature_creation.py", line 321, in process_single_file scan_df = process_mgf_file( File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/inspire/input/mgf.py", line 44, in process_mgf_file with mgf.read(mgf_filename) as reader: File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/mgf.py", line 458, in read return tp(args, kwargs) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/mgf.py", line 290, in init super(IndexedMGF, self).init(source, parser_func=self._read, pass_file=False, args=(), kwargs={}, File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/mgf.py", line 131, in init super(MGFBase, self).init(source, kwargs) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/auxiliary/file_helpers.py", line 1020, in init super(TaskMappingMixin, self).init(args, *kwargs) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/auxiliary/file_helpers.py", line 380, in init super(TimeOrderedIndexedReaderMixin, self).init(args, kwargs) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/auxiliary/file_helpers.py", line 401, in init super(IndexedTextReader, self).init(source, mode='rb', encoding=None, kwargs) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/auxiliary/file_helpers.py", line 199, in init self.reset() File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/auxiliary/file_helpers.py", line 204, in reset self._source = _file_obj(self._source_init, self._mode, self._encoding) File "/home/martin.pasen/Code/prosit-library-reanalises/.venv/lib/python3.8/site-packages/pyteomics/auxiliary/file_helpers.py", line 102, in init self.file = codecs.open(f, mode, encoding) File "/usr/lib/python3.8/codecs.py", line 905, in open file = builtins.open(filename, mode, buffering) FileNotFoundError: [Errno 2] No such file or directory: 'data/prosit1/measurements/01974c_BA1-TUM_missing_first_1_01_01-2xIT_2xHCD-1h-R4/controllerType=0 controllerNumber=1 scan=32948.mgf'

[jamc1996]

Hi Martin,

Thanks for pointing it out. We were assuming mascot users would be using mscovert with the scan title editted to include the source name but we should have insure it would work for the default settings.

The PR linked should address the issue, you should be able to install the tarball attached also if you want to get moving before it's merged and published on pip.

For this case you will need to specify: ``` sourceFileName: ``` in your config file. Thanks for using inSPIRE! Best wishes, John.

[martinPasen]

Thanks for the fast response. The problem seems to prevail even after implementing the proposed changes.

[jamc1996]

For anyone reading this in future we were able to resolve this issue. I have deleted the tar file from the earlier message. The corrected file is:

inspirems-1.1.tar.gz

However, it should be published on pip in the next few days and calling

pip install inspirems

will automatically download version 1.1.

[jamc1996]

Version bump is now published on pypi so the default

pip install inspirems

should download the correct version.

If you are experiencing this issue and already have inspirems==1.0 install please call

pip install inspirems --upgrade

Thanks Martin for raising this issue!