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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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Problem with MSFragger: java.lang.OutOfMemoryError: Java heap space #119

Closed cesarrivera closed 3 years ago

cesarrivera commented 3 years ago

Hello community, I had a problem with MSFragger: "java.lang.OutOfMemoryError: Java heap space"

My computer: Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz 3.19 GHz 32 GB RAM

MSfragger version: 13.0 Philosopher version: 3.3.11 (build 1601497354) Python version: Python 3.7.6

Global settings: RAM: 0 (auto) Parallelism: 12 timsTOF LC/MS files

Database: The Human Oral Microbiome Database (All) http://www.homd.org/ftp/genomes/PROKKA/current/faa/ALL_genomes.faa 1.9 GB, 2.8 GB (.pepindex file)

Can I fix it by increasing the JAVA virtual memory? Is the base too big for my computer?

I added my log file.

log_2020-12-09_10-11-41.txt

Thank you very much for your help,

César Rivera Talca, Chile

fcyu commented 3 years ago

Although your computer have 32 GB RAM in total, there were only about 23 GB free memory according to FragPipe. To analyze timsTOF data, we suggest having 32 GB ~64 GB free memory available.

Best,

Fengchao