Roger Volden

Do you have Cython installed? `pip3 install --user Cython` should do the trick. To cover all of your bases, try `pip3 install --user --upgrade Cython setuptools wheel`. Then you can...

Can you follow the debug step seen here: https://github.com/rvolden/C3POa/issues/17#issuecomment-783469536 For some reason python multiprocessing doesn't like passing back errors, so it'll just die silently instead of complaining.

Seems to be a problem with pyabpoa, can you verify that your install is working correctly? It may have installed but it could still run into runtime errors

Yeah, we took out that option since ONT qscores are mostly nonsensical

That's weird that on your first run, it didn't align with blat but still ran? So I'm guessing that wasn't your first run and it had already produced the psl...

Weird how it goes straight from the `Aligning` message to the traceback. Something that doesn't make sense is that the directory it's saying for the splint isn't right. It's saying...

Yeah that's weird - I haven't seen that error before. Looks like blat is limited to 17Gb of memory usage. I'm not sure how I haven't seen that before. I'm...

Just pushed a preprocessing version where it chunks the input for parallelized blat. This should hopefully get around your input file size and it'll speed up the preprocessing considerably.

Remove the output and try it again with `-n 10`. I tested with lower thread numbers and it causes multiprocessing to throw an error.

C3POa will chunk the fastq and write temporary fastas for the blat alignment. When you use `-n 10`, it should split your input fastq into 10 chunks, which should take...