I have a question when exporting taxonomic assignment using MEGAN6 through command-line. I actually use the following line to calculate lower-common ancestor for each contig (as input I accept up to 100 contigs to nr-viral using diamond blastx).
megan6/tools/blast2lca -a2t ../prot_acc2tax-May2017.abin -i Contigs.protein.txt --format BlastTab -o Contigs.protein.lca
As output I get taxonomic assignment of each contig individually including all taxonomic levels so that some contigs start at order level while orders are directly categorized at species level.
But, when using MEGAN6 with graphic interface there is an option to export TaxaIDtoContigID which you can export at diferent taxonomic levels which contigs are categorized within each taxa. Is that possible through command-line operations?
Thank you so much!