SystemError: <class 'Fasta'> returned a result with an error set; on loading gzipped fasta

[jolo2486]

When loading e.g. the below gzipped fasta file: hgdownload.cse.ucsc.edu/goldenPath/dp3/bigZips/dp3.fa.gz

I get:

fasta = pyfastx.Fasta('./data/genomes/dp3.fa.gz')
RuntimeError: get seq count and length error

The above exception was the direct cause of the following exception:

Traceback (most recent call last):

  Cell In[61], line 1
    fasta = pyfastx.Fasta('./data/genomes/dp3.fa.gz')

SystemError: <class 'Fasta'> returned a result with an error set

I am in a conda environment, and installed pyfastx 0.9.1 using pip.

• Ubuntu 22.04.2 LTS
• conda 23.1.0
• python 3.8.16
• pyfastx 0.9.1

[lmdu]

First, delete the previous generated index file dp3.fa.gz.fxi, and then use pyfastx.Fasta to reindex it. If this does not work, please let me known.

[maximilianmordig]

Still fails.

The issue persists, even after deleting the index file (fxi file) curl https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz -O. It seems to be related to the index though:

import pyfastx; pyfastx.Fasta("chm13v2.0.fa.gz", build_index=False)

works, but

import pyfastx; pyfastx.Fasta("chm13v2.0.fa.gz")

does not.

I am using pyfastx version 1.1.0