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yeeus / GCI

A program for assessing the T2T genome continuity
MIT License
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Killed the command #11

Open JesseBNL opened 1 month ago

JesseBNL commented 1 month ago

Dear yeeus,

I think this is an excellent tool to map the depth and gaps of an assembly, but it does not succeed for me. It keeps killing the command after running for a while:

Finding gaps ...
Finding gaps done!!! The gaps are in ../final_assemblies/GCI.gaps.bed

Filtering HiFi alignment files ...
Filtering HiFi alignment files done!!!
Writing depths into "../final_assemblies/GCI_hifi.depth.gz" ...
Writing depths done!!!

Filtering ONT alignment files ...
Killed

Also when I try to plot the hifi depth using the generated GCI_hifi.depth.gz file and the stand-alone utility, it kills the command. Can the memory management for this script be optimized?

yeeus commented 1 month ago

Actually, this problem was caused mainly due to memory usage which was metioned in the To do section of README. And the solution is always increasing your memory allocation. I'm sorry for the memory issue again. and I wish someday I would improve it!