Closed Lizzie-Roeble closed 2 months ago
Hi Lizzie,
Hmm, looking at the code, I think this might be a bug that can occur when the outgroup sequences for a given taxon have identical sequence identity to one of the ingroup sequences. Is that a possibility with your dataset?
Would you be comfortable sharing your input data and command for the failed run, so I can double check this and push a bugfix? If so, you could email it to me directly at chris.jackson@rbg.vic.gov.au.
Cheers,
Chris
Hi Chris,
Yes - the issue was an ingroup sample being closely related to the outgroup. This was not intentional...the ingroup sample was mislabeled. I now have had a chance to rerun with the sample removed, and ParaGone runs as expected.
Thanks! Lizzie
Fixed in version 1.1.0
Hi, I am having an issue in the align_selected_and_tree step, specifically with align_selected_and_tree.py and the
seq_to_keep
variable:I am running paragone with 3 internal outgroups and version 0.0.14rc (July 2023)
I am testing the sensitivity of different outgroups, and my other paragone runs/outgroups have run smoothly.
Any thoughts on what is causing this issue? Let me know if you need any more information. Thanks, Lizzie