eXpress runs out of memory

pachterlab / kma

Keep Me Around: Intron Retention Detection

GNU General Public License v2.0

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Open julsssen opened 8 years ago

julsssen commented 8 years ago

Hi,

does anyone know how much memory eXpress normaly requires. I am running 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. Does anyone know, how much I would need to run at least one sample?

edkonyakhina commented 6 years ago

Hi @julsssen,

Did you find a solution of this problem? I have the same and I don't know, what to do with it.

Many thanks, Evgeniya

julsssen commented 6 years ago

Hi, no sorry, I stopped trying to get eXpress to work. I got an answer in a different forum https://groups.google.com/forum/#!msg/express-users/rDPDIFrnTV4/fyGcApqRCgAJ

"Disabling bias correction should greatly reduce the memory usage for you."

I don't no if this is helpful or not for you, I did not try.