bbuchfink
diamond sscinames are the same as staxids
hi, I built Diamond database using; diamond makedb --in nr.gz \ –db nr_diamond –taxonmap prot.accession2taxid.FULL –taxonnodes nodes.dmp –taxonnames names.dmp
And then I run the blastx as followed: diamond blastx --db nr.dmnd --query samples.fasta -o samples.txt -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames staxids sscinames sskingdoms
However when I check the output (samples.txt) I did not find any Subject Scientific Name(s), also the Subject Super Kingdom(s) and the Subject Kingdom(s), but the taxid. Here is the example of my output
"ODE_3310_length_540_cov_1.123711 UVH34328.1 98.4 123 2 0 128 496 1 123 2.33e-79 242 28344 28344 28344 28344 10239"
It seems like those are taxid but not names
I download the prot.accession2taxid.FULL, nodes.dmp and names.dmp followed by the WiKi.
Any suggestions?
Looking foward to your reply.
Did you notice the following output when you built database? I had the same problem for weeks. Taxonomy names are not loaded.
Loading taxonomy names... [0.591s]
Loaded taxonomy names for 0 taxon ids.
Did you notice the following output when you built database? I had the same problem for weeks. Taxonomy names are not loaded.
Loading taxonomy names... [0.591s]Loaded taxonomy names for 0 taxon ids.
hi, yes, I have the same problem when I check the log file of makedb.
I have downgraded the version to 2.0.9 and I have found that this problem has been solved. I guess you can have a try. I don't know whether is because of the version. I used 2.1.6 before but it did not work.
