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fix empty bin_info.tsv with --skip-abundances #127
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Looks like you need to update the second merge as well. For safety, it should likely be a left join as well to keep all of the checkm output, also should change the column it is joining on to on=[merged_out.columns[0]]
right?
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Just in case taxonomy is missing a genome?
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Yep, I know there are cases where GTDB-tk will randomly fail to assign taxonomy to genomes due to some pplacer issue. Not sure what happens to the gtdb-tk output in that case, like it might just end up missing from the file. Additionally, there probably exists a world where running gtdb-tk ends up being an optional step so making it a left join future proofs against that I suppose
Manual test running now |
Manual test succeeded |
Noooooo |
Into main again :( |
haha it's okay, just catch dev up to main |
My bad. Inner join removes all the other bin info...