Classify.otu command

[Shayak]

Hello everyone,
I am new to this field and using Mothur for the first time. I am using mothur v.1.48.0. I am currently facing an issue with the classify.otu(list=final.opti_mcc.list, count=final.count_table, taxonomy=final.pds.wang.pick.taxonomy, label=0.03)
0.03 command. When I run the command, I am getting the following warning messages:

[WARNING]: ERR9763156.10010 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.30372 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.13925 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.10013 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.5825 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.26697 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.13911 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.3660 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.7628 is not in your taxonomy file. I will not include it in the consensus.
[WARNING]: ERR9763156.4673 is not in your taxonomy file. I will not include it in the consensus.

I have followed the Mothur SOP, but I might be missing something. Could anyone help me understand what might be going wrong? Any guidance on troubleshooting this would be greatly appreciated!

Thanks in advance!

[pschloss]

Hey there,

Welcome! It looks like you may have run something like remove.lineage on your taxonomy file without including the count file or the fasta file. The list and count_table files don’t have the “pick” tag in their file names which makes me think you may have your files out of sequence.

Pat