I'm using Mugsy to align 120 genomes but I encounter an error during the execution, the message is:
Could not run system command: : Cannot allocate memory
cat /../mugsy_wga_test/mugsy_out/tmpprojections.out | /source_installers/mugsy_x86-64-v1r2.2/synchain-mugsy 1000 30 30 > 62003lcbs.out 2> 62003synchain-mugsy.out
Does anyone have encountered this error and how did you solved? Or does anyone have any insights on what might be the reason for this error?
Thank you
It looks like you're running out of memory. Either your machine doesn't have enough RAM for running the task or some other process is competing for it or there's a memory leak. Use the top or ps commands to see what's eating up the memory e.g.
I didnt expect that to be the problem, the server has 64GB in RAM, which I think is enough to do this task, even though I recompiled mugsy (I used the precompiled version) and I'm doing the alignment again to see what happens.
Thanks for your suggestion I didnt know of the ps command.