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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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MSBooster finished when using LFQ-phospho workflow #1672

Closed michellefai closed 3 months ago

michellefai commented 3 months ago

- Upload your log file

log_2024-07-15_10-14-20.txt

- Describe the issue or question: Do you have any suggestion to overcome 'FileParsingException' caused by java.util.concurrent.TimeoutException? I am uploading the raw file to perform LFQ-phospho workflow.

Your feedback is much appreciated. Thanks

yangkl96 commented 3 months ago

Hello,

Is it possible to increase the amount of RAM? You currently only allocated 15GB.

Best, Kevin

michellefai commented 3 months ago

Hello,

Thanks for your reply. The max RAM capacity of my pc is only 16 GB. What do you think?

yangkl96 commented 3 months ago

If you do not have access to a computer with more RAM, you could try running just the MSBooster step multiple times, each time with a different subset of your files (3 or 4 subsets should be sufficient). Once they are all completed, you can run the remaining downstream steps with all files together

yangkl96 commented 3 months ago

You can also replace the old C:\Users\User\Downloads\FragPipe-jre-22.0\fragpipe\tools\MSBooster-1.2.31.jar with the a pre-release jar file here: https://github.com/Nesvilab/MSBooster/releases/tag/v1.2.38

This version requires less memory, potentially enough of a decrease for you to run it on your current computer