Mugsy can not allocate memory

Question

[rafa.rios.50]

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

[Jean-Karim Heriche]

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.

ps --sort -rss -eo rss,pid,command | head

[rafa.rios.50]

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.

Answer 1

[rafa.rios.50]

I solved the problem, but the solution is not perfect because I am still getting other errors.

What I did was to download the source code of Mugsy and re compile it. The compilation was a little buggy, there was a patch in the sourceforge repositories which worked well.

Now I have an error about Nucmer and its inability to parse the delta and filtered delta files. I have used an absolute path when executing Mugsy. But even though these errors, Mugsy ended and a MAF alignment was obtained. I'm not really sure if those missing files/analysis could create a troublesome alignment.