I started Yaamini’s PECAN run on a subset of samples and wanted to document the pecanpie command I use. I gave it access to 12 of the 16 logical cores on Roadrunner, and 30gb of the 48gb of available ram to hopefully avoid the complete non-functionality that is currently afflicting Emu.
pecanpie -o /home/srlab/Documents/DNR_PECAN_Run_3_output -s gigas -n DNR_oyster_SpLibrary --pecanMemRequest 30 /home/srlab/Documents/DNR_PECAN_Run_3_20170308/2017-03-08-mzML-file-path-list.txt /home/srlab/Documents/DNR_PECAN_Run_3_20170308/2017-03-08-background-peptides-path-list.txt /home/srlab/Documents/DNR_PECAN_Run_3_20170308/2017-03-03-isolation-windows.csv --fido --jointPercolator --isolationSchemeType BOARDER --overwrite
The –overwrite is only there because I ran it once before forgetting the spelling of “BORDER” used so I had to tell it to overwrite the directory already created.
After this I moved to /home/srlab/Documents/DNR_PECAN_Run_3_output and ran ./run_search.sh which spooled up the jobs properly with Grid Engine.
Looking at qstat -f and top it looks like it is running properly. Hopefully we’ll get some results in some tractable amount of time.