Problem when running MSFragger on Mac

Hi authors,

Thanks for MSFragger. But I get the following error when trying to run MSFragger on my Mac (M1 pro, Ventura 13.3):

java -jar MSFragger-3.7.jar open_fragger.params_edited data/W_N18/*.d

MSFragger version MSFragger-3.7 Batmass-IO version 1.28.9 [main] ERROR umich.ms.fileio.filetypes.bruker.Timsdata - JNA could not load native Bruker library [main] ERROR umich.ms.fileio.filetypes.bruker.Timsdata - The ext folder with timsdata-2-21-0-4.dll (Win) or libtimsdata-2-21-0-4.so (Linux) is needed. If you are using an old ext folder, please upgrade. timsdata library version (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: Mac OS X, Architecture: x86_64 Java Info: 11.0.18, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 8 GB memory Checking database... Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000 Parameter 'ion_series_definitions' was not supplied. Using default value: Parameter 'Y_type_masses' was not supplied. Using default value: Parameter 'diagnostic_fragments' was not supplied. Using default value: Checking spectral files... Failed in checking /Users/vy/Downloads/MSFragger-3.7/data/W_N18/wash_homemade_column0812_one_column_Slot1-02_1_1861.d. Will ignore it. Bruker native libraries not found. If you are using Windows, please make sure that Visual C++ Redistributable for Visual Studio 2017 (https://aka.ms/vs/16/release/VC_redist.x64.exe) is installed. If you are using Linux, please maks sure that all dependencies are installed (can check using ldd command). Failed in checking /Users/vy/Downloads/MSFragger-3.7/data/W_N18/wash_homemade_column0812_one_column_Slot1-02_1_1861.d. Will ignore it. Bruker native libraries not found. If you are using Windows, please make sure that Visual C++ Redistributable for Visual Studio 2017 (https://aka.ms/vs/16/release/VC_redist.x64.exe) is installed. If you are using Linux, please maks sure that all dependencies are installed (can check using ldd command). Failed in checking /Users/vy/Downloads/MSFragger-3.7/data/W_N18/W_N18_20220916_Neoantigen_HM0812_one_column_Slot1-45_1_1864.d. Will ignore it. Bruker native libraries not found. If you are using Windows, please make sure that Visual C++ Redistributable for Visual Studio 2017 (https://aka.ms/vs/16/release/VC_redist.x64.exe) is installed. If you are using Linux, please maks sure that all dependencies are installed (can check using ldd command). Failed in checking /Users/vy/Downloads/MSFragger-3.7/data/W_N18/wash_homemade_column0812_one_column_Slot1-02_1_1862.d. Will ignore it. Bruker native libraries not found. If you are using Windows, please make sure that Visual C++ Redistributable for Visual Studio 2017 (https://aka.ms/vs/16/release/VC_redist.x64.exe) is installed. If you are using Linux, please maks sure that all dependencies are installed (can check using ldd command). /Users/vy/Downloads/MSFragger-3.7/data/W_N18/wash_homemade_column0812_one_column_Slot1-02_1_1863.d: Scans = 0 /Users/vy/Downloads/MSFragger-3.7/data/W_N18/wash_homemade_column0812_one_column_Slot1-02_1_1862.d: Scans = 0 /Users/vy/Downloads/MSFragger-3.7/data/W_N18/wash_homemade_column0812_one_column_Slot1-02_1_1861.d: Scans = 0 /Users/vy/Downloads/MSFragger-3.7/data/W_N18/W_N18_20220916_Neoantigen_HM0812_one_column_Slot1-45_1_1864.d: Scans = 0 There are corrupted files. Please remove those files and re-start the task.

I got to know that MSFragger can run on Mac, but it seems that the Bruker library is not available (in the zip) for MacOS. And the software can really detect MacOS but it keeps giving instructions for Windows users.

In the same folder: ls -la

total 139016 drwxrwxr-x@ 17 vy staff 544 Apr 6 17:47 . drwx------@ 8203 vy staff 262496 Apr 6 17:40 .. -rw-r--r--@ 1 vy staff 6148 Apr 6 17:36 .DS_Store -rwxrwxr-x@ 1 vy staff 57084253 Jan 12 16:17 MSFragger-3.7.jar -rw-rw-r--@ 1 vy staff 68024 May 14 2022 MSFragger-LICENSE-3RD-PARTY.txt -rw-rw-r--@ 1 vy staff 69467 Jan 28 2020 MSFragger-LICENSE.pdf -rw-rw-r--@ 1 vy staff 14018 Jan 12 10:44 Nglyco-HCD_fragger.params -rw-rw-r--@ 1 vy staff 107720 Sep 2 2019 RawFileRdr_License_Agreement_RevA.pdf -rw-rw-r--@ 1 vy staff 41725 Sep 2 2019 THIRD-PARTY-LICENSE-README.txt -rw-rw-r--@ 1 vy staff 9957 Jan 12 10:44 closed_fragger.params drwxr-xr-x 4 vy staff 128 Apr 6 17:13 data drwxrwxr-x@ 5 vy staff 160 Apr 6 17:36 ext -rw-rw-r--@ 1 vy staff 9957 Jan 12 10:44 nonspecific_fragger.params -rw-rw-r--@ 1 vy staff 9956 Jan 12 10:44 open_fragger.params -rw-rw-r--@ 1 vy staff 9791 Apr 6 17:47 open_fragger.params_edited -rw-rw-r--@ 1 vy staff 342 Sep 2 2019 redist.txt -rw-r--r--@ 1 vy staff 13714782 Mar 1 09:43 uniprot-dna-rna-zmc054.fasta

May I have any suggestions for this? Thanks in advance!

Bests, Vy

Nesvilab / MSFragger

Problem when running MSFragger on Mac #258