FAMSA hangs on identical sequences

refresh-bio / FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

GNU General Public License v3.0

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FAMSA hangs on identical sequences #34

Closed arvestad closed 4 months ago

arvestad commented 2 years ago

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 commented 2 years ago

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

agudys commented 2 years ago

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

arvestad commented 2 years ago

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