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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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Subject super kingdoms is "0" #466

Open zhaoxvwahaha opened 3 years ago

zhaoxvwahaha commented 3 years ago

Hi, I have some quesionts about the "subject super kindoms " when specify the -outfmt "6 ... sskingdoms", the following are the type of sskingdoms in my output, what's the difference between 0 and N/A, and why some subjects have more than 1 sskingdoms?

0 0;Bacteria;Eukaryota 0;Eukaryota Bacteria Bacteria;Eukaryota N/A

Thanks in advance

bbuchfink commented 3 years ago

N/A means that the target sequence does not have any taxids assigned to it.

0 can mean that the target's taxon id is not mapped to a taxonomic rank (possibly the mapping files could be inconsistent). It can also mean that the path in the taxonomy from the target's taxon id to the root does not pass through a superkingdom node.

In databases like the NR for example, target sequences often have more than one accession, so they can have multiple taxon ids possibly belonging to different superkingdoms. You can use the staxids field to see the taxon ids of the target sequence.

zhaoxvwahaha commented 3 years ago

@bbuchfink Got it, thank you so much helpful reply.