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FAMSA hangs on identical sequences #34

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arvestad opened this issue Sep 13, 2022 · 3 comments
Open

FAMSA hangs on identical sequences #34

arvestad opened this issue Sep 13, 2022 · 3 comments
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@arvestad
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FAMSA (version 2.1.2- (2022-08-04) installed using conda) hangs without progress if I run it on a set of identical sequences (but different accessions). Editing a single sequence to a different residue will make FAMSA to behave as intended. Using the option --keep-duplicates is also a work-around.
@agudys agudys self-assigned this Sep 15, 2022
@agudys agudys added the bug label Sep 15, 2022
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agudys commented Sep 15, 2022

Hello @arvestad,
Thank you for reporting the issue. I'll do my best to fix it soon!
Regards,
Adam

agudys added a commit that referenced this issue Sep 30, 2022
@agudys
Fixed incorrect handling of single sequence sets (missing first resid…
bffb731 
…ue) or sets containing only duplicates (hang) (#34)
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agudys commented Sep 30, 2022

Hello @arvestad!

The bug has hopefully been fixed in the latest commit. Please let me know if it works (you would need to build the binary from the sources, though - it is not on bioconda yet).

Best,
Adam

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arvestad commented Oct 2, 2022

Thanks, I cannot prioritize this for a few days unfortunately.

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