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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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so looong!! #49

Open julieaorjuela opened 3 years ago

julieaorjuela commented 3 years ago

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 commented 3 years ago

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