The bioBakery help forum

Calculate taxonomy table from 'genefamilies.tsv'

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!

Sorry for the late reply - infer_taxonomy was disabled in HUMAnN 3.alpha versions but is re-enabled in the 3.0.0 release, so you could try upgrading and using that?