As others have noted, using classify.seqs with the SILVA database provided you get the top 6 levels:
M03580_15_000000000-AHFYP_1_2115_20833_19910 Eukaryota(100);Opisthokonta(100);Holozoa(100);Metazoa_(Animalia)(100);Eumetazoa(100);Bilateria(100);
But if you make your own taxonomy file you can get more:
grep '>' silva.nr_v123.align | cut -f1,3 -d$'\t' | cut -f2 -d'>' > silva.nr_v123.long.tax
M03580_15_000000000-AHFYP_1_2115_20833_19910 Eukaryota(100);Opisthokonta(100);Holozoa(100);Metazoa_(Animalia)(100);Eumetazoa(100);Bilateria(100);Arthropoda(100);Crustacea(100);Maxillopoda(100);Copepoda(100);Calanoida(100);unclassified;unclassified;unclassified;
What are the things that will break downstream by having more than 6 levels in these files?