OSError: [Errno 12] Cannot allocate memory

[Former user]

Hi

I'm trying to run OncodriveFML with the "-s wes " flag on my machine with 800GB of RAM and I'm getting the following error: File "/home/diogopell/.local/lib/python3.6/site-packages/oncodrivefml/scores.py", line 117, in enter self.mm = mmap.mmap(self.fd.fileno(), 0, access=mmap.ACCESS_READ) OSError: [Errno 12] Cannot allocate memory

My input MAF file has 2.4M and my regions file has 75M. Is it normal?

[Diogo Pellegrina]

well, its been a while!

In the end I chopped my intervals file in a hundred pieces and ran each one separately (but with the same mutations table). It worked but was not ideal. My other post still baffles me

[Iker Reyes]

Should not be normal but it might depend on how you define your regions (although 800 GB is quite a lot). OncodriveFML is analyzing each region separately and loading all the score from the same region. If you define huge regions it might be that you run out of RAM. You can also try to reduce the number of cores used so less regions are analyzed at the same time and thus less memory is used