Intermittent Pyfastx Errors (`corrupted size vs. prev_size`, `free(): invalid next size (fast)`)

[JeanMainguy]

Hey,

First off, thanks for creating this great tool!

I'm using pyfastx in Binette, and some users have run into occasional errors like:

• corrupted size vs. prev_size
• free(): invalid next size (fast)

The issue was reported here: genotoul-bioinfo/Binette#49

It doesn’t happen all the time, which makes it tricky to reproduce, but it seems related to the index file when using pyfastx.Fasta. In Binette, I open the same input contig file twice and store the index file in a temporary directory inside the output directory to avoid cluttering the original location.

To work around this, I changed how pyfastx is used to only call pyfastx.Fasta once at the end when it's really needed and use pyfastx.Fastx otherwise (see genotoul-bioinfo/Binette#52). So far, this seems to prevent the issue on my side.

Do you have any idea what might be causing this and if there’s a more reliable fix?

Thanks a lot for any insights!

[lmdu]

Thanks for reporting this issue. I will check that.

[JeanMainguy]

Hi,
Another Binette user just ran into the same error again: genotoul-bioinfo/Binette#58.
Do you have any ideas on how we could fix this?

Thanks a lot!