ProtMap getting stuck - Githubissues

CWRU-CPB / ProtMapMS

ProtMapMS is a search engine for protein footprinting experiments.

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ProtMap getting stuck #4

Closed rohitmpibpc closed 4 years ago

rohitmpibpc commented 5 years ago

Hi Sean,

I tried to run ProtMap on 4 LC-MS runs. The analysis was for trypsin digestion and complex of 2 proteins. The program ran fine when i used 0 ms and 10 ms/0 ms and 20 ms/0 ms and 30 ms. It yielded close to 35 peptides. But the program got stuck for hours when i attempted to run all exposures together. Could you help with this issue ?

Thanks, Rohit

many-states commented 5 years ago

It sounds like it might be running out of memory. Try changing the launch command to:

java -Xmx2g -Xms2g -jar ProtMapMS.jar --gui

So that the JVM initializes with a 2GB heap.

rohitmpibpc commented 4 years ago

Hi Sean,

I tried changing the run.bat file with above command. I was not able to open it. Could you please help ? I could not attached original run.bat file here. It will be great if you could modify it. I will try to run sample here.

Rohit