search

kbaseattic / assembly

An extensible framework for genome assembly.
MIT License
12 stars 14 forks source link

Dev #290

Closed sebhtml closed 9 years ago

sebhtml commented 9 years ago

This will close

https://github.com/kbase/assembly/issues/244

levinas commented 9 years ago

Awesome. One question about memory usage:

I'm not sure how the memory option is being interpreted by megahit. Is it mindful of what the available memory is? I wonder if we need to cap the memory at:

system_memory / total_threads * process_threads_allowed

sebhtml commented 9 years ago

I added the requested change.

sebhtml commented 9 years ago

I ran into this problem BTW: I expected self.process_threads_allowed to be an integer (int). However it is a string. I was multiplying a string and it took me some time to figure this out.

levinas commented 9 years ago

I'll run a manual test by replacing all the a6 assembler with megahit in arast.t.

sebhtml commented 9 years ago

OK. let me know all it goes.