Using the tblastx to blastx change of line 1 also worked with the nucl_acc2tax-May2017.abin mapping file, using a script. An earlier attempt with mapping file, using the graphical interface, did not work, but I have not tested again.
If someone wants to include the following 2 lines in a bash script (I used a Refseq database for blast, identifiers start with "ref|", $ID is the first part of the filename, $MAPfile is the full path to nucl_acc2tax-May2017.abin):
perl -pi -e 's/TBLASTX/BLASTX/' $ID.tx.out
/opt/megan/tools/blast2rma -i $ID.tx.out -f BlastText -bm BlastX -r $ID.fna -o $ID.txmap.rma6 -c -lg -a2t $MAPfile -atags "gb| ref| refseq|"
For me this does the job, and if I want to check an alignment I can do that in the blast output, so I do not have another request than 'just' to include the option that it can be used for tblastx, too.
Daniel, if you still want to have a fasta-tblastx_out combination to play with, I can send it to you directly