I’m quite new with MEGAN6 and I’m not sure if there exists any not-binary reference files. I have a contig that using diamond blastx matches to protein reference:
contig-3000000 ref|YP_002004542.1| 31.4 175 108 5 1454 942 164 330 5.7e-18 94.7
This reference can actually be found in NCBI nr database (https://www.ncbi.nlm.nih.gov/protein/YP_002004542), but MEGAN6 does not assign any taxonomy to it. And we don’t know why. How can I check if this NCBI nr sequence exists in the prot_acc2tax file? We are also wondering problems related to the bitscore 94.7 as MEGAN sets a threshold to 95. Is that correct?
Any idea would be very thankful,