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Bug with pyfastx in f2 train [with solution]

#59Openedwhisnant 创建于 2026-04-28
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edwhisnantcommented
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.
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