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WGLab / LIQA

Long-read Isoform Quantification and Analysis
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Out of memory problem #36

Closed sonyuna90 closed 3 months ago

sonyuna90 commented 11 months ago

Hi I have this issue and I have allocated my hpc memory to 150gb currently. Is there any better way to do this process?

Thanks!

liqa -task diff

DAS testing: Gene MIR99AHG being processed...Error : cannot allocate vector of size 135.7 Gb slurmstepd: error: Detected 1 oom-kill event(s) in StepId=10538082.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.

agouru55 commented 4 months ago

Hi - maybe either (1) distributing memory across threads https://github.com/WGLab/LIQA/pull/28 if possible or (2) try filtering out low-confidence reads before quantifying and analyzing.