Problem with read counts in daa2rma

I am having some trouble using the tool daa2rma from MEGAN6. I have some .daa files obtained from Diamond blastx. When using this code:

megan/tools/daa2rma -i input.daa -o output.rma -lg -alg longReads \
-a2t prot_acc2tax-May2017.abin -a2interpro2go acc2interpro-Nov2016XX.abin

I get .rma files whith a read assignment mode of alignedBases instead of readCounts (which seems to be the default value for -ram parameter).

Am I doing something wrong? Any ideas?



alignedBases is the default in the long-read mode, as the read length can vary a lot for long-reads.


P.S.: you can also use daa-meganizer, which won’t create a new RMA file, but instead append classifications to the existing daa file.