respre memory issue

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itair
Posts: 2
Joined: Sun Apr 24, 2022 2:23 pm

respre memory issue

Post by itair »

Hi,
I have a memory issue with respre:
currently I have memory limit of 20 GB on my machine.
when I try to run ResPRE it get killed with messege such as:
/usr/bin/respre: line 2: 65 Killed python /ResPRE/respre.py $@
or:
/usr/bin/respre: line 2: 20 Killed python /ResPRE/respre.py $@
alignment of 74 proteins, 1145 letters in each protein (including gaps)

I tried to look at old successful runs and I found out that I got max memory usage of ~ 550 GB.
I think the high usage is short-termed, possibly a leak of some kind.
Is there some kind of a workaround / solution for this?
Thanks!
Itai Roth
itai.roth@evogene.com
liyangum
Posts: 5
Joined: Tue May 11, 2021 1:42 am

Re: respre memory issue

Post by liyangum »

Hi,

Thank you for the feedback. Can you send us the MSA? ResPRE may use large memory with long sequences, but it should not reach up to 550G.
You can also send me the MSA by email.

Thanks,
Yang Li
itair
Posts: 2
Joined: Sun Apr 24, 2022 2:23 pm

Re: respre memory issue

Post by itair »

Hi,
Thank you for the reply.
Unfortunately I cannot send you the MSA since the data is a property of private institute.
However, I will try to describe it:
protein MSA,
5451 sequences
654 AA per sequence ( un gapped length is about 136 AA)
Itai
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