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anvi-get-sequences-for-hmm-hits fails to report HMM hits for internal genomes #955

meren opened this Issue Sep 3, 2018 · 1 comment


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meren commented Sep 3, 2018

This is a critical bug that is associated with anvi'o v5.1.

When anvi-get-sequences-for-hmm-hits, which is extensively described here as a part of the anvi'o phylogenomics workflow, is used with internal genomes, the resulting FASTA file does not consider collection names for internal genomes.

When the user also uses --concatenate and --return-best-hit flags, the resulting FASTA file for a given bin contains genes that are best hits for a given gene name not only in the bin itself, but in the entire contigs database, likely resulting in critical mistakes in phylogenomic analyses.

@meren meren added bug priority labels Sep 3, 2018

@meren meren self-assigned this Sep 3, 2018

@meren meren closed this in 461f1d7 Sep 3, 2018


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meren commented Sep 3, 2018

The issue is now resolved in master.

If you have been using anvi'o v5.1 for phylogenomic analyses with internal genomes, you have two options:

[Sane approach] Use only external genomes

If you want to stick with the stable version, don't use internal genomes file, and instead only use external genomes file. To do that, run anvi-split on your collection, and use the path for resulting contig databases, each of which are now specific to your internal genomes in your external genome files.

[Less sane approach] Switch to the master repository

You can also switch to the master repository as it is described here, and redo your analyses.

Please ask if you have any questions with this. Anvi'o developers apologize sincerely in case this bug caused any inconvenience to you.

Thanks for your patience.

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