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so looong!! #49

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julieaorjuela opened this issue Feb 16, 2021 · 1 comment
Open

so looong!! #49

julieaorjuela opened this issue Feb 16, 2021 · 1 comment

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@julieaorjuela
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Hello,
I wonder why smartdenovo is so looong ??!!
I have reserved 10 CPU and 100G per CPU. I have 52G of data (ONTreads >=10Kb) and launched
by default parametters using build_conda_envs/3f08aa12/bin/wtzmo -t 8 -i SMART.fa.gz -fo SMART.dmo.ovl -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000
It has beeing running from 10 days :S
At the moment, I have 55G of SMART.dmo.ovl and 17G of SMART.fa.gz.
Do you think it will be finish a day? How to estimate how many time is required to smartdenovo assembly?
Any idea?
Thanks.
Julie
@ruanjue
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ruanjue commented Feb 16, 2021

Not sure.

Try to increase CPU numbers, or change the overlapper from zmo to dmo.

smartdenovo.pl -e dmo -t 32 SMART.fa.gz  >run.makefile

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@julieaorjuela @ruanjue