pmenzel
commented
6 years ago Hi,
it is intended behavior: kaijuReport puts all reads assigned to viruses in the same generic bin.
There were some issues some time ago that gave weird output for viruses when selecting -r genus or -r family, so I changed it to the current behaviour.
If you need full taxon paths for viruses, then please use the output of kaiju2krona.
./kaijuReport -t kaiju_db/kaiju_index/nodes.dmp -n kaiju_db/kaiju_index/names.dmp -i RefSeq_13_S28.kaiju.out.csv -r species -o RefSeq_13_S28.kaiju.out.summary
I'm getting there lines for viruses:
` % reads species
3.420722 1661 Alistipes finegoldii 0.988529 480 Bacteroides cellulosilyticus 0.683733 332 Bacteroides fragilis 0.595177 289 Bacteroides thetaiotaomicron 0.570464 277 Bacteroides ovatus 0.313034 152 Bacteroides caecimuris
66.775131 32424 Viruses 3.562823 1730 cannot be assigned to a species
21.152461 10271 unclassified ` It seems, that kaiju can't split viruses to speies in report file, but able to do in in krona file.