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Old 04-05-2016, 01:26 PM   #1
julsssen
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Location: UK

Join Date: Apr 2016
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Question Memory requirments for eXpress

Does someone know how much memory eXpress usually consumes? (https://github.com/adarob/eXpress)

I am using eXpress together with kma (https://github.com/pachterlab/kma)

But I run out of memory after a few minutes when I a run:

express -o 2monthsCTX/WT/WT1/xprs_out annotation/mm10_and_introns.fa \
2monthsCTX/WT/WT1/mm10.bam

my mm10_and_introns.fa has 3.6 gb
and my mm10.bam file has 9.2 gb

I have 42GB allocated RAM on my virtual Linux machine.
Is it possible that this is not enough RAM for one sample, or is it more likely that something else is wrong?

Many thanks for any help.
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Old 04-06-2016, 04:52 AM   #2
GenoMax
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Are you getting a message about running out of memory?
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Old 04-06-2016, 05:33 AM   #3
julsssen
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Hi, yes kind off: the message is : killed
I have a resource viewer (htop) open at the same time. It happens when I ran out of memory. No other message unfortunatly.
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Old 04-06-2016, 05:38 AM   #4
GenoMax
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Just checking that you did install 64-bit linux on the VM? Does the program get killed right away or after some time?
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Old 04-07-2016, 02:59 AM   #5
julsssen
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Hi, yes 64bit Linux.

It does not get killed straigth away, but after the the 42 GB ram are full, then it writes onto the swap for a second, then get killed.
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