Hi,
When running humann3, I used ‘.sam’ files with no header annotation as input. However, only returned ‘genefamilies.tsv’ files.
Is there any solution to calculate a taxonomy table in genus or species level from ‘genefamilies.tsv’ files? The function ‘humann_infer_taxonomy’ in humann3 seems to be valuable but doesn’t work.
The header of my sam files:
DP8400017160BRL1C035R05401581835/2 16 39491__A0A173RWU4__ERS852417_03173|k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Lachnospiraceae.g__Lachnospiraceae_unclassified.s__Eubacterium_rectale|UniRef90_A0A173RWU4|UniRef50_W7BZN9|645 335 6 100M * 0 0 CTCACGTACAGGATCTCGCAAAGTATGCTTCTCCTATCGTTTCGTGCGGTAATCAGACCGGTGAGGGCTGGTTTTTGACAGGTGAGATGCTTGAGCTCAT A=B<==D@CC@<CBE;A?D7BC=>D8DDB2B=9=DC5@D@C<1CA>9DC=AD:BB<8?;?CB8;B@:CB6CC.C>CB@ADDADDB@BC?CBB?B<B?@B: AS:i:-15 XS:i:-20 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:7G12G22T56 YT:Z:UU
DP8400016951TRL1C033R01601262235/1 0 204516__U6RFW1__HMPREF1534_02572|k__Bacteria.p__Bacteroidetes.c__Bacteroidia.o__Bacteroidales.f__Bacteroidaceae.g__Bacteroides.s__Bacteroides_massiliensis|UniRef90_U6RFW1|UniRef50_R6DAX6|1215 408 42 100M * TGCCGTACTCTGCATTCCCGGCTCGGGTATGACAAAAGAAAACCTCATCGGAGAAGTTTCCGCCAACAATATGCGGGCGGCTATGGCCTTAAACATTGCA FCFHHDIHGEFFGHGGFHGFEHFHFGCDGGHFGGFFEFDHFGGIGFHGHFEEHDFFGFGHGEHIGEGHGGHIEGDEIGGHAGFFHFGGHEFEGGFFHGGG AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21A78YT:Z:UU
Thank you!