Linux: Fragpipe Headless Thermo Native Libraries Not Detected

[Sanpme66]

** Log file**

Fragpip_Linux.zip

Issue Description:
Thank you for the FragPipe Linux CLI release.

I'm encountering an error related to raw file I/O; it appears that the "Batmass-IO binaries for Thermo support and/or Thermo native libraries" are not found.

Steps taken:

• Downloaded MSFragger-4.0 and included its directory path using --config-msfragger.
• Did the same for --config-philosopher and --config-python, following a similar resolution from someone who encountered a similar error. MSFragger-4.0 contains Thermo and Bruker libraries.

The raw file is from Thermo Fisher Mass Spectra.

Command used in the shell:

./bin/fragpipe --headless --workflow /canelib/raw_data/tools/fragpipe/test/data/output/fragpipe.workflow --manifest /canelib/raw_data/tools/fragpipe/test/data/output/fragpipe-files.fp-manifest --workdir /canelib/raw_data/tools/fragpipe/test/data/output --config-philosopher /canelib/raw_data/tools/fragpipe/tools/philosopher --config-python /canelib/raw_data/tools/fragpipe/py3.9/bin/python3 --config-msfragger /canelib/raw_data/tools/fragpipe/tools/MSFragger-4.0/MSFragger-4.0.jar > test/data/output/logs.log

Could you please review the log file attached?

Thank you!

[fcyu]

Have you installed mono according to the tutorial here https://fragpipe.nesvilab.org/docs/tutorial_setup_fragpipe.html ?

If yes, could you run mono /canelib/raw_data/tools/fragpipe/tools/MSFragger-4.0/ext/thermo/BatmassIoThermoServer.exe, and send me the screenshot?

Thanks,

Fengchao

[Sanpme66]

Yes! You're right. The mono toolkit was missing during installation, which caused the issue. It's now up and running smoothly.

Thanks for the response!

Have you installed mono according to the tutorial here https://fragpipe.nesvilab.org/docs/tutorial_setup_fragpipe.html ?

If yes, could you run mono /canelib/raw_data/tools/fragpipe/tools/MSFragger-4.0/ext/thermo/BatmassIoThermoServer.exe, and send me the screenshot?

Thanks,

Fengchao