I know this isn't an MS-GF+ support board, but the main site at UCSD hasn't
been updated in quite a while and I'm not aware of an official board for
it. Since I think some TPP users also use MS-GF+, I thought I'd try here to
see if anyone has ideas.
I recently began running MS-GF+ on a Windows (64-bit) machine, and the
searches are running extremely slowly. For a single 3.5 hr QExactive run (~
48k spectra) against a NextProt database with semitryptic search, 2 missed
cleavages, and Oxidized M as the only variable mod it's taking 6+ hours per
file. When I was using MS-GF+ under Linux a similar search would take 30-40
minutes.
My MS-GF+ command is as follows:
java -Xmx10G -jar C:\TPP\bin\MSGFPlus\MSGFPlus.jar -s {mzloc} -o {outfn} -d
..\..\dbase\nextprot_all_DECOY.fasta -t 20ppm -thread 14 -ti "-1,2" -tda 0 -m
3 -inst 3 -e 1 -ntt 1 -mod mods.txt
I've tried setting threads and -Xmx much higher, but they don't seem to
have any effect. CPU usage hovers at 8-9% with memory usage for the java
process around 2GB.
The system is a Xeon E5-2695 @ 2.30 GHz with 56 virtual cores and has 192
GB RAM. I have Oracle java Version 8 Update 73 (64-bit of course).
Has anyone else solved an issue, or is there something boneheaded in my
parameters?
Jason
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