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Possible to lower memory usage for haslr_assemble #11
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I got the farthest with this command
But, after a little while I got the same error as #5 , even though I was only using 75% RAM at most. |
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Hi,
I have a single node Ubuntu 16.0.4 system with 378 GB RAM and 40 cores (80 threads). During the
haslr assemble
stage, memory usage jumps to 100 % andhaslr_assemble
starts using Swap, so I dropped--cov-lr
from 25 to 20 to 15 and now to 10. The genome is 450 Mbp with ~ 30x PacBio CLR (simulated reads) and ~60x Illumina short-reads (simulated). I will see if the the--cov-lr 10
setting works on my system (i.e., it doesn't use too much RAM before completion), but I was wondering if there might be some way to minimize RAM usage during this step. Any ideas?Update:
--cov-lr 10
ran out of memory as well, so I am playing around with--aln-block
and--aln-sim
settings (was using defaults)The text was updated successfully, but these errors were encountered: