Bug with pyfastx in f2 train [with solution]

[edwhisnant]

Hi,

I noticed a bug with pyfastx that was leading to an inability to do the QC checks at the beginning of the f2 train. I thought it might have been an issue with my assembly, so I split my assembly in two and found that there was no issue with pyfastx loading and reading the split files separately. There was no obvious issue with the assembly. I moved directly into the directory with the fasta file and ran pyfastx while I was in the directory and it also worked fine.

Turns out pyfastx seems to have a limit on the length of the input name (for example, if you provide a long absolute path). A temp fix was to just add a cd to move into the directory with the assembly file and avoid using the absolute path. This resolved the issue.

[edwhisnant]

Note: I should have been more clear that a really long file name (not just simply a long path) will also cause this error.

[nextgenusfs]

Seems bizarre, hard to imagine what the issue would be with a long file path? Probably best to open issue upstream in pyfastx

[edwhisnant]

okay so I was able to exclude long file paths as the issue. It has nothing to do with that. The issue arises from long file names. I confounded my attempted fixes by adding the cd and then making a temp copy with a shorter name. I will mention this in pyfastx