Can never get fragger to run without memory crash

[AmandaSmythers]

- 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.)

- Describe the issue or question:
I have tried using MS Fragger for a variety of purposes over the years, but regardless of what I do, it always crashes and says it doesn't have enough memory. This time I have 9 timsTOF DDA files, limited variable mods, decreased max peptide size, and split database up to 24 times, but it still happens every time. My computer has 64 gb ram and a 16 core processor.

logs.zip

[fcyu]

Keep increate the "split database" in the "MSFragger" tab until it works.

Best,

Fengchao

[AmandaSmythers]

I have tried this, all the way up to 150 splits and it still doesn't work. This is a normal mouse proteome, nothing crazy. Surely this cannot be the reason.

[anesvi]

What workflow are you using, actually? And what database? Regular search should be totally fine with 64gb and without splitting

[fcyu]

When you increase the "split database", you need to set "calibration and optimization" to "None" as suggested at the end of the log file:

If mass calibration was enabled, please turn it off by setting calibrate_mass = 0 (when running MSFragger in command line) or changing 'calibration and optimization' to 'None' (when running MSFragger in FragPipe).

Best,

Fengchao

[anesvi]

Well, if you follow GitHub instructions, it starts with " upload the log file"... something is not right since you seem to be doing a standard search that many people do just fine.

[fcyu]

You shares 9 log files. Could you point me the one with 150 splits?

Also, it would be better not to manually set the "RAM" in the workflow tab, because you likely don't know the right amount of free memory in your computer.

Best,

Fengchao

[AmandaSmythers]

I am doing a custom workflow, where the majority of the defaults remain the same. I change the cysteine mod to a different static mod that we use. I am using the mouse database downloaded from uniprot and used the MSFragger interface to add contaminants and decoys, with a final total of 172166 entries.

I already set calibration and optimization to none several attempts ago. I followed all of the instructions at the end of the log, but none helped.

[fcyu]

Could you set "RAM" back to "0" in the workflow tab, set "calibration and optimization" to none, run FragPipe, and share the log file?

Thanks,

Fengchao

[AmandaSmythers]

I definitely understand that this shouldn't be an issue, but I have followed instructions - unless I am missing something! I have tried to troubleshoot this in the past and consulted my peers. Here is a log where I set the ram to automatic ( "0" ) and used 150 database splits. Cal/optimization is none. I truly appreciate your help.

log_2025-04-01_12-00-08.txt

[fcyu]

Thanks for sharing the log file. I think something was wrong with your operating system's environment variable, because it overwrote FragPipe's memory setting. In your log file:

['java', '-jar', '-Dfile.encoding=UTF-8', '-Xmx32G', WindowsPath('C:/Users/ADMIN/Downloads/FragPipe-22.0/fragpipe/tools/MSFragger-4.1/MSFragger-4.1.jar'), 'fragger.params', WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib1_S6-D4_1_413.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib2_S6-D5_1_414.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib3_S6-D6_1_415.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib4_S6-D7_1_416.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib5_S6-D8_1_417.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib6_S6-D9_1_418.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib7_S6-D10_1_419.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib8_S6-D11_1_420.d'), WindowsPath('C:/Users/ADMIN/Desktop/Taylor_DDA_Lib/DDA_lib9_S6-D12_1_421.d'), '--partial', '0']
Picked up _JAVA_OPTIONS: -Xmx1024M
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: Windows 10, Architecture: AMD64
Java Info: 16.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 1 GB memory
Checking database...

It only allows FragPipe and MSFragger to use 1024 MB memory....

Best,

Fengchao

[AmandaSmythers]

Thank you! this is super helpful. I will work to see how I can fix this.