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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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make: *** [pwk_genome.mak:27: pwk_genome.dmo.cns] Error 137 #57

Open dzh0220 opened 1 year ago

dzh0220 commented 1 year ago

Hi Ruanjie,

Thank you very much for the excellent work in developing Smartdenovo for the genome assembly.

I tried to assemble a mouse genome with Smartdenovo by running it with the command below. The program crashed with the error attached. I wonder if you have any advice on to deal with it.

command

error snapshot

Thanks, Zhenhai

ruanjue commented 1 year ago

There should be a bug in wtcns, please run it part by part.

seq 0 99 | xargs -i echo wtcns -t 32 -i pwk_genome.lay -o pwk_genome.cns.{}.fa -P 100 -p {} >cns.sh

run the cns.sh one by one line or send each a job on cluster, then find which one/ones riases error again. After locate the error part, you can invoke more parts like 1000 to further locate it.

dzh0220 commented 1 year ago

Hi Jue,

I just realized I misspelled your name! Sorry about this!

Thank you very much for your quick reply! I will try to locate the error according to your advice.

BTW, in the description of smartdenovo, you claimed that wtcorr would be very slow for large genomes. As I am trying to assemble a mouse genome with a size of about 2.7GB, do you think it will be better to try wtdbg2?

Thanks again! Zhenhai

ruanjue commented 1 year ago

First, wtcorr is not necessary in smartdenovo. Second, wtdbg2 would be better to assemble lage/huge genomes.

dzh0220 commented 1 year ago

Thank you so much! wtdbg2 worked!!

Zhenhai