Error when filling in missing precursor info: ufunc 'isnan' not supported for the input types #207
Description
Hi,
I'm re-analyzing the immunopeptidomics data from the Thunder DDA-PASEF paper with Sage, and performing rescoring with MS2Rescore / TIMS2Rescore (v3.1.4), but I get the following error below.
I'm not entirely sure what the issue is, but seems to be an error when checking for retention and ion mobility? I have looked at the rt and ion_mobility columns in the input file (results.sage.tsv), but they don't contain any NaNs.
Best,
Justin
TIMS²Rescore (v3.1.4)
MS²Rescore tuned for timsTOF DDA-PASEF data.
Developed at CompOmics, VIB / Ghent University, Belgium.
Please cite: Declercq & Devreese et al. bioRxiv (2024)
2024-12-10 15:56:01 INFO ms2rescore.parse_psms // Reading PSMs from PSM file
(1/1): 'results.sage.tsv'...
2024-12-10 15:57:26 INFO ms2rescore.parse_psms // Removed 0 PSMs with rank
>= 10.
2024-12-10 15:57:29 WARNING ms2rescore.parse_psms // Removed 2 PSMs with
invalid amino acids.
2024-12-10 15:57:42 INFO ms2rescore.parse_psms // Found 1152514 PSMs, of
which 29.02% are decoys.
2024-12-10 15:57:49 WARNING ms2rescore.parse_psms // Non-mapped modifications
found: {'-18.010565', '+42.010567', '+119.0041',
'-17.026548'}
This can be ignored if they are Unimod modification
labels.
2024-12-10 15:57:54 INFO ms2rescore.core // Found 335390 identified PSMs
with rank <= 1 at 0.01 FDR before rescoring.
2024-12-10 15:57:57 INFO ms2rescore.core // Parsing missing retention time
and/or ion mobility values from spectra...
2024-12-10 16:02:40 ERROR ms2rescore.__main__ // ufunc 'isnan' not supported
for the input types, and the inputs could not be
safely coerced to any supported types according to
the casting rule ''safe''
╭─────── Traceback (most recent call last) ───────╮
│ /home/singjust/.local/lib/python3.11/site-packa │
│ ges/ms2rescore/__main__.py:237 in main │
│ │
│ 234 │ │ │ profiled_rescore = profile(re │
│ 235 │ │ │ profiled_rescore(configuratio │
│ 236 │ │ else: │
│ ❱ 237 │ │ │ rescore(configuration=config) │
│ 238 │ except Exception as e: │
│ 239 │ │ LOGGER.exception(e) │
│ 240 │ │ sys.exit(1) │
│ │
│ /home/singjust/.local/lib/python3.11/site-packa │
│ ges/ms2rescore/core.py:65 in rescore │
│ │
│ 62 │ ) │
│ 63 │ │
│ 64 │ # Add missing precursor info from spe │
│ ❱ 65 │ psm_list = _fill_missing_precursor_in │
│ 66 │ │
│ 67 │ # Add rescoring features │
│ 68 │ for fgen_name, fgen_config in config[ │
│ │
│ /home/singjust/.local/lib/python3.11/site-packa │
│ ges/ms2rescore/core.py:198 in │
│ _fill_missing_precursor_info │
│ │
│ 195 │ │ if required and ( │
│ 196 │ │ │ 0.0 in psm_list[value_name] │
│ 197 │ │ │ or None in psm_list[value_nam │
│ ❱ 198 │ │ │ or np.isnan(psm_list[value_na │
│ 199 │ │ ): │
│ 200 │ │ │ if all(v is None or v == 0.0 │
│ 201 │ │ │ │ raise exceptions.MissingV │
╰─────────────────────────────────────────────────╯
TypeError: ufunc 'isnan' not supported for the
input types, and the inputs could not be safely
coerced to any supported types according to the
casting rule ''safe''