IndexError: list index out of range

[Mar10L]

Hi. I am getting the same error:

Traceback (most recent call last):
  File "/iga/scripts/dev_modules/mambaforge/envs/duet-v0.6/bin/methphasing", line 1471, in <module>
    main(sys.argv[1:])
  File "/iga/scripts/dev_modules/mambaforge/envs/duet-v0.6/bin/methphasing", line 1396, in main
    [0], phased_region_list[1][0])]
IndexError: list index out of range

The command that I used was this one:

meth_phaser_parallel -t 10 -ml -2 \
-o methphaser \
-b grapevine.minimap2.filtered_only_primary.bam \
-r reference.fasta \
-g grapevine_phased.whatshap.stats.gtf \
-vc grapevine.clair3.phased.vcf.gz

Theoretically, I should not have problems with sex chromosomes, given the fact that grapevines do not possess them.

Thank you in advance for the help.

Originally posted by @Mar10L in https://github.com/treangenlab/methphaser/issues/10#issuecomment-1780631353