Hi!
I keep running into the following warning message when running classify.otu. I ran this exact same data a few weeks ago and this didn’t happen. I haven’t changed the batch file at all so I’m not sure what is causing it to appear now. It is excluding over 26,000 sequences.
mothur > classify.otu(list=BMD_bact_2.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.pick.opti_mcc.unique_list.list, count=BMD_bact_2.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.abund.pick.count_table, taxonomy=BMD_bact_2.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.pds.wang.pick.taxonomy, label=0.03)
0.03 28998
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_19291_10575 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_8950_8530 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_16404_2944 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_16729_32869 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_11954_6740 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1107_13529_12345 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_18102_6338 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_7689_8869 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_5531_2596 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_17921_6086 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_20412_4162 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_8274_16142 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: HISEQ_414_HCHT3BCXY_1_1101_3788_5405 is not in your taxonomy file. I will not include it in the consensus.
Thank you!
Kelsy