Sage with TimsTOF Data Rescoring

[jonathan-krieger-bruker]

Hello,

I am trying to run a rescore with Sage results and timsTOF data.

My configuration for Rescore and the error I receive is as follows.

oktoberfest -c ./oktoberfest_rescore_config.json
2025-02-21 16:19:23,837 - INFO - oktoberfest.utils.config::read Reading configuration from ./oktoberfest_rescore_config.json
2025-02-21 16:19:23,837 - INFO - oktoberfest.runner::run_job Oktoberfest version 0.8.3
Copyright 2025, Wilhelmlab at Technical University of Munich
2025-02-21 16:19:23,837 - INFO - oktoberfest.runner::run_job Job executed with the following config:
2025-02-21 16:19:23,837 - INFO - oktoberfest.runner::run_job {
"type": "Rescoring",
"tag": "",
"output": "./out",
"inputs": {
"search_results": "./results.sage.tsv",
"search_results_type": "Sage",
"spectra": "../",
"spectra_type": "d",
"instrument_type": "TIMSTOF"
},
"models": {
"intensity": "AlphaPept_ms2_generic",
"irt": "AlphaPept_rt_generic"
},
"prediction_server": "koina.wilhelmlab.org:443",
"numThreads": 30,
"fdr_estimation_method": "mokapot",
"add_feature_cols": "none",
"regressionMethod": "spline",
"ssl": true,
"thermoExe": "ThermoRawFileParser.exe",
"massTolerance": 20,
"unitMassTolerance": "ppm",
"ce_alignment_options": {
"ce_range": [
19,
50
],
"use_ransac_model": false
}
}
2025-02-21 16:19:23,837 - INFO - oktoberfest.utils.config::read Reading configuration from ./oktoberfest_rescore_config.json
2025-02-21 16:19:23,838 - INFO - oktoberfest.preprocessing.preprocessing::list_spectra Found 3 d directories in the spectra input directory.
2025-02-21 16:19:23,838 - INFO - oktoberfest.runner::_preprocess Converting search results from results.sage.tsv to internal search result.
2025-02-21 16:19:23,838 - INFO - spectrum_io.search_result.search_results::generate_internal Found search results in internal format at out/msms/msms.prosit, skipping conversion
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/oktoberfest/bin/oktoberfest", line 8, in
sys.exit(main())
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/main.py", line 40, in main
runner.run_job(args.config_path)
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/runner.py", line 1378, in run_job
run_rescoring(config_path)
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/runner.py", line 1249, in run_rescoring
spectra_files = _preprocess(spectra_files, config)
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/runner.py", line 77, in _preprocess
timstof_metadata = pp.convert_timstof_metadata(
File "/home/ubuntu/miniconda3/envs/oktoberfest/lib/python3.10/site-packages/oktoberfest/preprocessing/preprocessing.py", line 592, in convert_timstof_metadata
raise ValueError(f"Unsupported search engine provided for reading timstof metadata: {search_engine}")
ValueError: Unsupported search engine provided for reading timstof metadata: sage

Thank you for your help!
Jonathan