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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 #10 (comment)
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