Why do you have nucleotides in the taxonomy file? Are they in the feature ID? They shouldn’t be processed as nts anyway, right?
From the feature classifier tutorial (greengenes);
# FeatureData[Taxonomy]
229854 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Legionellales; f__Legionellaceae; g__Legionella; s__
367523 k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Flavobacteriaceae; g__Flavobacterium; s__
239330 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfuromonadales; f__Geobacteraceae; g__Geobacter; s__
203525 k__Bacteria; p__OP11; c__OP11-1; o__; f__; g__; s__
148318 k__Bacteria; p__ZB3; c__; o__; f__; g__; s__
340276 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
289157 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
# FeatureData[Sequence]
>1111561
AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCACGCCTAACACATGCAAGTCGAACGGCAGCGGGGGAAAGCTTGCTTTCCTGCCGGCGAGTGGCGGACGGGTGAGTAATGCGTAGGAATTTGCCATTAAGAGGGGGACAACTCGGGGAAACTCGAGCTAATACCACATAATCTCTTCGGAGCAAAGAAGGGGATTCTTCGGAACCTTTCGCTTAATGAGAAGCCTACGTTGGATTAGCTTGTTGGTGGGGTAAAGGCTCACCAAGGCGATGATCTATAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTGGACAATGGGGGAAACCCTGATCCAGCGATGCCGCGTGTGTGAAGAAGGCCTAAGGGTTGTAAAGCACTTTTAGTGAGGAAGAGAGTAAGTCGGTTAATACCCGGCTTGCAAGACGTTACTCACAGAAAAAGCGCCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGATTGACTGGGCGTAAAGGGCGCGTAGGCGGTAAGATAAGTCAGATGTTAAAAACCCGAGCTCAACTTGGGGACTGCATTTGAAACTATCTCACTAGAGTACAGTAGAGGAGAGCGGAATTTCCGGTGTAGCGGTGAAATGCGTAGATATCGGAAGGAACACCAGTGGCGAAGGCGGCTCTCTGGACTGACACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGAACTAGCTGTTGGTACGTTTAGTATCAGTAGCGCAGCTAACGCGTTAAGTTCTCCGCCTGGGGATTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGCGGTTTAATTCGATGCAACCCGAAAAACCTTACCTACCCTTGACATCCCGCGAAGCCTGTAGAGATACGGGCGTGCTCGAAAGAGAACGCGGTGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTGTCCTTAGTTGCCATCTACATTAGTAGGGAACTCTAAGGAGACTGCCGGCGATAAGTCGGAGGAAGGTGGGGACGATGTCAAGTCATCATGGCCTTTATGGGTAGGGCTACACGCGTGCTACAATGGGCAGTACAAAGGGAAGCGAAGCTGTGAAGTGGAGCAAACCTCAGAAAGCTGCTCGTAATCCGGATTGAAGTCTGCAACTCGACTTCATGAGGTTGGAATCGCTAGTAATCGCAGATCAGCATGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGAAGTGGGTTGTACCAGAAGTAGGAGAGCTAACCTTCGGGAGGCATCTTACCACGGTATGATTCATGACTGGGGTGAAGTCGTAACAAGGTA
>1111421
GAGTAACGCGTAGGAACCAACCTTAGAGAGTGGAATAACCTTGGGAAACTAAGGCTAATACCGCATATACCTCGAGAGGGAAAGGAGAGTAATCTCTGCTCTAGGACGGGCCTGCGCCCGATTAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCATCGATCGGTAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCTTGATCCAGCCATGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTTTCACACGCGACGATGATGACGGTAGCGTGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGTCTAATTTGTCGGGGGTGAAATCCCAGGGCTTAACCTTGGAAGTGCCTTCGGGACAATTAGGCTTGAGACCGGGAGAGGATGGCGGAATTCCCAGTGTAGAGGTGAAATTCGTAGATATTGGGAAGAACACCGGTGGCGAAAGCGGCCATCTGGTCCGGTTCTGACGCTAAAGCGCGAAAGCGTGGGGGAGCGAACAGGATTAGATACCCTGGTAGCCACGCCGTAAACGATGTGTGCTGGATGTCGGGGGGCATGCTCTTCGGTGTCGTAGCTAACGCGTGAAGCACACCGTCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGAACCTTACCAGCCTTTGACATGCCCTTTATATCCTAAAGAGACTTGGGAGTCGGTTCGGCCGGAAGGGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATTCTCAGTTGCCATCGGGTCATGCCGGGCACTCTGAGGGGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTACAGGCTGGGCTACACACGTGCTACAATGGCGGTGACAATGGGTTATCAGGCGACTCTGCGAAGAGGAGCGAATCCTAAAAGACCGTCTTAGTTCGGATTGCACTCTGCAACCCGGGTGCATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGTCTTTACTCGAAGACAGTGTGCCAACCTTAA
>1111090
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGGGTTTAACACATGCAAGTCGAGGGACGAAACCATCTTCGGATGGCTGAAACCGGCGAACGGGTGAGTAACACGTGACCAACCTGCCCTTCACTCAGGGATAACAGCGGGAAACCGTTGCTAACACCTGATACCGCGAGTCGAGCGCATGCTCTTCTCGTGAAAACTCCGGTGGTGAAGGAGGGGGTCGCGGCCTATCAGGTAGTTGGTGCGGTAACGGCGCACCAAGCCGACGACGGGCAGCTGGAGTGAGAGCTCGAGCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGAGAATCTTGCACAATGGGCGAAAGCCTGATGCAGCCACGCCGCGTGGAGGAAGAAGGCCTTCGGGTTGTAAACTCCTTTCAGCAGGGAAGAAGCGAAAGTGACGGTACCTGCAGAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGTGTAGGCGGACCATTAAGTCGGCTGTGAAATCTCTGGGCTCAACCCAGAAACTGCAGTCGATACTGGTGGTCTTGAGGTAGCTAGAGGAGAGTGGAATTCCCAGTGTAGCGGTGGAATGCGCAGATATTGGGAGGAACACCAATGGCGAAGGCAGCTCTCTGGAGCTCACCTGACGCTGAGACGCGAAAGCATGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGGGTGCTAGATGTGGGGACCAGTTCACGGTCTCCGTGTCGAAGCTAACGCGTTAAGCACCCCGCCTGGGGACTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGCTTAATTCGAAGCAACGCGAAGAACCTTACCTAGTCTTGACATACACCGTTCAACTACCGAAATGTAGTGGGTTCGTCCGAGGTGTACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTATGTTGCCAACACGTAATGGTGGGGACTCATGGGAGACTGCCGGTGTCAAACCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGCCCCTTATGACTAGGGCTGCACACATGCTACAATGGCAGGTACAGAGGGCTGCGATCCCGCGAGGGGGAGCGAATCCCACAAAGCCTGTCTCAGTTCGGATTGCAGTCTGCAACTCGACTGCATGAAGCCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCCAACCCTTCATTGGGGGGGAGCCGTCTAAGGTGGGATCGGTAATTGGGACGAAGTCGTAACAAGGTAGCCGTA
>1110893
TCCTGGCTCAGATGAACGCTAGCGCGGAGGCTTAATACATGCAAGTCGAACGGTAACAGGTAATTTATTATGCTGACGAGTGGCGCACGGGTGAGTAACGCGTACATACCTACCTCTAAGAAAGGAATAGCCCTGGGAAACTGGGATTAATACCTTATGTGCTGGTGACAGTAAAGCTACGGCGCTTAGAGATGGATGTGCGTTCTATTAGCTAGTTGGTGAGGTAACTGCTCACCAAGGCGACGATAGATAGGGGGCGTGAGAGCGTGATCCCCCACACGGGTACTGAGACACGGACCCGACTCCTACGGGAGGCAGCAGTAAGGAATATTGGACAATGGGCGGAAGCCTGATCCAGCCATCCCGCGTGTAGGAAGACTGCCCTATGGGTTGTAAACTACTTTTAGACAGGAAGAAACGCCTTTATTTATGAGGGTTTGACGGTACTGTCAGAATAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGATACGGAGGGTGCAAGCGTTATCCGGAATCACTGGGTTTAAAGGGTGAGTAGGCGGGTTATTAAGTCAGAGGTGAAAGGTTTCAGCTTAACTGCAAAATTGCCTTTGATACTGATAGTCTAGAATTATGTTGAGGTTAGCGGAATGAGTCATGTAGCGGTGAAATGCATAGATATGACTTAGAACACCAATTGCGAAGGCAGCTAACTGGGCATATATTGACGCTGAGTCACGAAAGCGTGGGGAGCGAACAAGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGCTAACTCGATGTTTGTTTAAATATGAGCATCCAAGGGAAACCGTTTAGTTAGCCACCTGGGGAGTACGTTCGCAAGGATGAAACTCAAAGGAATTGACGGGGGTCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGATACGCGAGGTACCTTACCTGGGCTCTAATGCGCGTGACCGCTTCTGAAAGGAAAGCTTTCCTTCGGGACAAAGCAAGGTGCTGCATGGTTGTCGTCAGCTTCGCGCCGTGAGGTGTTGGGTTAAGTCCTGCAACGAGCGCAACCCCTATTGTTAGTTACCAGCAAGTAAGTTGGGGACTCTAGCAAGACTGCCGGCGTAAGCCGCGAGGAAGGTGGGGATGACGTCAAATCATCATGGCCTTACGTCCTGGGCTACACACGTGCTACAATGGTAGGTACAGAGAGCAGCCACTACGCGAGTAGGAGCGAATCTATAAAACCTATCACAGTTCGGATCGGAGTCTGGAACTCGACTCCGTGAAGGTGGAATCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTCCCGGACCTTGTACACACCGCCCGTCAAGCCATGGGAGCTGGTGGTGCCTGAAGATGGTGACTTAACGTGGAGCTATTTAGGGTAAAACTAGTAACTGGGGCTAAGTCGTAACAAGGCTGCCGTACCGGAAGCGTGCGGCTGGATCACCTCCTT
>1110814
TTAGAGTTTGATCATGGCTCAGAACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCGAAAGGCTCCTTCGGGGGCCGAGTAGAGTGGCGAACGGGTGAGTAACACGTGGGTAACCTGCCCAAGAGCGGGGGACAACGTCGGGAAACCGGCGCTAATACCGCATACGCTTGTTCGGTTTTCGGATCGGACAAGGAAAGCCTTCGGGCGCTCCTGGATGGGCCCGCGTCGCATTAGCTTGTTGGTGGGATAACAGCCCACCAAGGCGACGATGCGTAGCCGAGCTGAGAGGCTGATCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCAACGCCGCGTGGGTGACGAAGGCCTTCGGGTCGTAAAGCCCTGTCGTGAGGGACGAAGTTCTGACGGTACCTCACAAGAAAGCCACGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGTGGCGAGCGTTGTTCGGAATCATTGGGCGTAAAGGGCGCGCAGGCGGCCCAGCAAGTCCGGGGTGAAAGCCCTCGACTCAATCGAGGAACGGCCTCGGAAACTGCTGGGCTTGAGTACGGGAGAGGTGAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCGGTGGCGAAGGCGGCTCACTGGACCGATACTGACGCTGAGGCGCGAAAGCCGGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCCGGCCGTAAACGTTGTGTACTAGGTGGTGGGGGTATCGACCCCTCCGCTGCCGCAGGTAACCCATTAAGTACACCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGCAGAACCTTACCCAGGCTTGACATCCCGCGCCATTCGGTGAAAGCCGGAGTTTCCTTCGGGAACGCGGTGACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTACCTGCTGTTGCTACCAGTTCGGCTGGGCACTCTGCAGGGACTGCCGGCGATAAGCTGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGCCCTTTATGTCTGGGGCTACACGCGTGCTACAATGGCCGATACAAAGGGTTGCCAACCCACGAGGGGGAGCCAATCCCAAAAAGTCGGCCTCAGTTCGGACTGGAGTCTGCAACTCGACTCCACGAAGGTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACCCGAATTGGCTGCACCCGAAGTCGTGTGCCCAACCGCAAGGAGGGTAGCGCCGAAGGTGTGGTTGGTAAGGGGGGTGAAGTCGTAACAAGGTAACCGTA
>1110088
AGAGTTTGATCATGGCTCACATTGCCCGCTGGCGTCATGCCTAACACATGCAAGTCCAACGGTAACGGGCCCTTCGGGGTGCTGACGAGTGGCGGACGGGTGAGTAATGCGACGGAATCTGCCTTACGGTGGGGGATAACCCGGGGAAACCCGGGCTAATACCGCATACGTCCCAAGGGAGAAAGCGGGGGATCTTCGGACCTCGCGCCGAAAGATGAGCCTACGTCCGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCGGTAGCTGGTCTGAGGGGATGATCAACCTCACTGGGACTGAGACTCCGTCCAGACTCCTACGGGAGGCTTCAGTGGGGAATTTTGGACAATGGGCTAAAGCCTGATCCTGCGATGCCGCGTGGGTGAAGAACGCCTTCGGGTTGTTCAGCCCTTTCGGCGGGGACGAAAATGCCGAACCTGATACCTTCGGGTCTTTGACGTTACCTGCGATAAGAAGCACCGGCTAACTCCGTGCCAGGCAGCCGCGGTAATACGGAGGGTGCTTGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTTTGTAAGTCATATGTGAAATCCCCGGGCTCATCCTGGGAACTGCATACTATACTGCTAGGTCTAGAGTGTGATAGAGGGAAGCGGAATTCACGGTCGTATCGGCGATTTGCGTATATATCCGGAGGATCTTCAGTGCCGTATGCTGCCTCACACGTACCAACACTGACGCTGAGGCGCGAACGCGTGAGGCAGCAAATCAGGATTAGGATATCCCTGGGTAGTCCACGCCGATAAACGACTGAGAAACTAGCCGATCTGGAAGTCAACTGGCTTTCTGGCTGGCGCAGCATAACGCGTTAAGTTGCTCCGCCTGGGGAGTACGGCCGCAACGGCATAAAACTCAAATGAATATGACGGGGGCCCGCACAAGCGGTGGAGTCATGTGGTTTAATTCGATGCAACGTCGAAAAACCTTACCTGCCCTTGACATCCTCGGAACTTGTCAGAGATTGACTTGGTGCCTTCGGGAACCGAGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTGTCCTTAGTTACCAGCGGTTCGGCCGGGAACTCTAGGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGATGTCGTCAAGTCATCATGGCCTTTATGTGCAGGGCTACACTCGTGCTACAATGGTCAGTTCAGAGGGAAGCCAACCCGCGAGGGGGAGGTAATCCCAGAAAATTGATCCTAGTCCGGATTGCAGTGTGCAAGTCGAATGCGTGAAGTCGGAATCGTTAGTAATCGGGAATCAGAATGTCGCGGTGAATACGTTCCCGGGCTTTGTACACGCCGCCCGTCACACCATGGGAGTGGGCTGTACCAGAAGCAGGTAGCCTAACGGTAAGGATGGCGCCTCCCACGGTGTGGTTCATGACTGGGGTGAATTTGTAACAAGGTAGCCGTA
>1109993
TTAGAGTTTGATCCTGGCTCAGGGTGAACGCTGGCAGCGTGCCTAATGCATGCAAGTCGAGCGGGGAGGGGAAACCCTCCCAGCGGCGAACGGCTGAGTAATATATAGCTGACCTACCCACCGGTGGGGGATAACCTCGGGAAACTGGGGCTAATACCGCATAATATAAGCTGGGGTGGTGCCTGGCTTATTAAAGCCCGCAAGGGCGCCGGTGGAGGGGGCTATATCTCAACAGGTAGTTGGTAGGGTAATGGCCTACCAAGCCTATGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCAGATGGGGACTGAGACACGGCCCCAACTCCTACGGGAGGCAGCAGCAGGGGATCTTGGGCAATGCCCGAAAGGGTGACCCAGCGACGCTGCGTGGGGGAAGAAGGCCTTCGGGTTGTAAACCCCTTTTGCCGGAGAAGAAGCTCTGACGGTATCCGGCGAATAAGCCTCAGCCAACTACGTGCCAGCAGCTGCGGTAAGACGTAGGAGGCGAGCGTTACCCGGAATTACTGGGCGTAAAAGGGATGTAGGTGGCCGATCAAGTCCGGGGTGAAATTTTCCGGCTCAACCGGGAAGCTGCTCCGGATACTGATTGGCTAGAGGGCATCAGGGGGAGACGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACGCCGATGGCGAAGGCGGTCTCCTGGGGTGCCCCTGACACTGAGATCCGAAAGCGTGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGGGCACTAGTTCTGGGGGGCACTGACCCCTCCCGGGACGAAGCTAACGCTTTAAGTGCCCTGCCTGGGGAGTATAGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCGTGTGGTTTAATTCGATGCAAAGCGTAGAACCTTACCAGGGCTTGACATGCCGGTAGTAGGAACCCGAAAGGGGGACGACTGGTATCCAGCCCAGAGCCGGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCTTAGTTGCATATCTAAGGGGACTGCCTCGCAAAACGGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCCCTTATGCCCTGGGCTACACACACGCTACAATGGACGCTACAGCGGGAAGCGACCGGGCGACCGGAAGCTGATCCCTTAAAAGCGTCCCCAGTTCAGATTGCAGGCTGAAACCCGCCTGCATGAAGCCGGAGTCGCTAGTAACCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCCTGTACACACCGCCCGTCACGGCATGGGAGCCGACAACACCTAAAAGCGCCAAGCTAACTCCACCGGAGAGGCAGGCGTCGAGGGTGAGGTCGGTGACTGGGCCGAAGTCGTAACAAGGTAACC