Question: Mugsy can not allocate memory
0
gravatar for rafa.rios.50
3.8 years ago by
rafa.rios.5060
Colombia
rafa.rios.5060 wrote:

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

whole genome alignment • 1.0k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by rafa.rios.5060

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
ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche21k

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.

ADD REPLYlink written 3.8 years ago by rafa.rios.5060
0
gravatar for rafa.rios.50
3.8 years ago by
rafa.rios.5060
Colombia
rafa.rios.5060 wrote:

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.

ADD COMMENTlink written 3.8 years ago by rafa.rios.5060
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