Batmass-IO binaries for Thermo support and/or Thermo native libraries not found
qussai96 opened this issue · comments
Dear Fengchao,
I am trying to run MSFragger on my Linux machine (Rocky Linux 8.6) using the following command:
java -Xmx64g -jar ~/Tools/MSFragger-3.6/MSFragger-3.6.jar /home/AT/0-raw_data/Proteomes/closed_fragger.params /home//AT/0-raw_data/Proteomes/01898_A01_P019768_S00_I00_N01_R1.raw
I am getting the following error:
MSFragger version MSFragger-3.6
Batmass-IO version 1.28.8
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: 11.0.13, OpenJDK 64-Bit Server VM, JetBrains s.r.o.
JVM started with 64 GB memory
Checking database...
Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000
Parameter 'activation_types' was not supplied. Using default value:
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 /home/AT/0-raw_data/Proteomes/01898_A01_P019768_S00_I00_N01_R1.raw. Will ignore it.
Batmass-IO binaries for Thermo support and/or Thermo native libraries not found
/home/AT/0-raw_data/Proteomes/01898_A01_P019768_S00_I00_N01_R1.raw: Scans = 0
There are corrupted files. Please remove those files and re-start the task.
I checked the MSFragger folder and it contains 'MSFragger-3.6.jar' and the 'ext' folder (with two subfolders: thermo and bruker).
I tried with two versions of MSFragger but still got the same error. Can you please let me know if you have any ideas why is that happening?
best,
Qussai
Hi Qussai,
Have you installed mono?
Best,
Fengchao
No, I had not installed it before. I just installed it and that fixed the problem.
Thank you very much.
best,
Qussai
You are welcome.
Best,
Fengchao