search

bacpop / ggCaller

Bifrost graph gene caller.
MIT License
86 stars 6 forks source link

Adds checks for removal of ORFs during scoring. #25

Closed samhorsfield96 closed 6 months ago

samhorsfield96 commented 6 months ago

Addresses out of range error, where occasionally multithreading will cause the same item to be remove from a map twice.

johnlees commented 6 months ago

The OS X tests are timing out here:

Fri, 24 Nov 2023 12:05:52 GMT 100%|██████████| 1/1 [00:00<00:00, 31300.78it/s]
Fri, 24 Nov 2023 12:05:55 GMT trimming contig ends...
Fri, 24 Nov 2023 12:05:55 GMT refinding genes...
Fri, 24 Nov 2023 12:05:55 GMT Number of searches to perform:  41
Fri, 24 Nov 2023 12:05:55 GMT Searching...
Fri, 24 Nov 2023 17:53:05 GMT Error: The operation was canceled.
samhorsfield96 commented 6 months ago

The OS X tests are timing out here:

Fri, 24 Nov 2023 12:05:52 GMT 100%|██████████| 1/1 [00:00<00:00, 31300.78it/s]
Fri, 24 Nov 2023 12:05:55 GMT trimming contig ends...
Fri, 24 Nov 2023 12:05:55 GMT refinding genes...
Fri, 24 Nov 2023 12:05:55 GMT Number of searches to perform:  41
Fri, 24 Nov 2023 12:05:55 GMT Searching...
Fri, 24 Nov 2023 17:53:05 GMT Error: The operation was canceled.

I've worked out why this is happening - the OSX implementation doesn't work with the python shared memory objects being used. I'm planning to rewrite these sections fully in C++ to avoid this issue entirely.