ContigIDtoTaxaID in command line


Hello Daniel,

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!


I have added a number of new features to the programs rma2info and daa2info and they give you quite a bit of control over what is output for a given file. For example, you can choose to output taxonomic names, paths or ids, and you can request that the rank is specifically listed on each line, making it easy to grep for specific ranks.
However, the programs don’t quite do what you want, that is, you can’t currently report for a given node on a given rank what is assigned to the node or below the node… I will look into this.