Specifying higher memory

[jchorl]

Hi!

I was processing an 8gb file with fastqc and was getting OOMs (Terminating due to java.lang.OutOfMemoryError: Java heap space). I bumped the memory up, but noticed fastqc limits ram to 10000 mb.

I then noticed that it allocates memory per-thread. By increasing thread count, I was able to hack it to have more ram and it succeeded. The thing is, in my case, I think it would make sense to just give it more ram with a single thread.

Does it still make sense to limit ram to 10000mb? Would you be open to converting the hard failure to a warning for overprovisioning ram?

[s-andrews]

If your file needs more than 10GB to process then the problem isn't allocating more RAM, there's something else which is problematic. Was this a nanopore file? Getting to the bottom of what consumed that much RAM would be a better fix.