Diagnostic ion mining workflow error (corrupted files)

[liangxiao023]

- Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

log_2024-07-17_11-21-30.txt

- Describe the issue or question:

Hi, I followed the tutorial (https://fragpipe.nesvilab.org/docs/tutorial_diagnostic_mining.html) to download the sample data and ran the process, but MSFragger reported the following error, can I ask what is the reason? It looks like it can't handle raw files, but why is that?

MSFragger [Work dir: /home/liangx/test] java -jar -Dfile.encoding=UTF-8 -Xmx741G /home/liangx/software/fragpipe/tools/MSFragger-4.1/MSFragger-4.1.jar /home/liangx/test/fragger.params /home/liangx/data/mRBS_dTamicon30K_4SU_HCD_half_1.raw MSFragger version MSFragger-4.1 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Linux, Architecture: amd64 Java Info: 11.0.1, OpenJDK 64-Bit Server VM, Oracle Corporation JVM started with 741 GB memory Checking database... Parameter 'analyzer_types' was not supplied. Using default value: all Checking spectral files... Failed in checking /home/liangx/data/mRBS_dTamicon30K_4SU_HCD_half_1.raw. Will ignore it. Could not get ThermoIndex There are corrupted files. Please remove those files and re-start the task. 2024-07-17 11:20:26 ERROR - Could not find Batmass-IO Thermo binary BatmassIoThermoServer from /home/liangx/software/fragpipe/tools/MSFragger-4.1/ext/thermo, /home/liangx/software/fragpipe/tools/MSFragger-4.1/./ext/thermo, /home/liangx/software/fragpipe/tools/MSFragger-4.1/../ext/thermo, /home/liangx/software/fragpipe/tools/MSFragger-4.1/../../../../ext/thermo, /home/liangx/software/fragpipe/tools/MSFragger-4.1/../../../../../ext/thermo /home/liangx/data/mRBS_dTamicon30K_4SU_HCD_half_1.raw: Scans = 0; ITMS: false; FTMS: false; Isolation sizes = [] Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping

[fcyu]

Could you upgrade FragPipe to 22.0 and try again?

Thanks,

Fengchao

[liangxiao023]

Could you upgrade FragPipe to 22.0 and try again?

Thanks,

Fengchao

Hi, thank you very much for your reply, I troubleshooted the error and found that the Mono software was deleted by someone else, and after installing it back it works fine, thank you.