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rpetit3 / dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
GNU General Public License v3.0
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Stuck in kmc part #5

Closed llk578496 closed 2 years ago

llk578496 commented 2 years ago

Hi @rpetit3 ,

Thank you for developing this tool! It is amazing.

I have just tried to run this tool, but sometimes it stuck in the kmc and doesn't continue running (I checked the cpu usage from htop). I quit the terminal and rerun again with option --force. The run will then be successfully completed. May I know how to solve this problem?

Thank you very much!

rpetit3 commented 2 years ago

Hi @llk578496,

Do you by chance know the genome size of the organism your assembling? If you do then you can use --gsize to skip the KMC step.

In the future I plan to replace KMC because it causes issues as well on my system.

llk578496 commented 2 years ago

Hi @rpetit3 ,

Yes, I am working on Enterococcus faecium which ranges from around 2.5 to 3.16 Mb. May I know it is ok to use 3.16 Mb for the --gsize?