cluster can't find seq name in count.table

Commands in mothur
1

Hi Guys

We have followed Pat’s MiSeq SOP to the letter and after making a dist file using dist.seq and then running cluster using the count cmd as well we get this, any suggestions, I think Mothur is having a hissy fit and linking two seq names together, even though the names are there in the table file.

can anyone help?

mothur > cluster(column=gm.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.dist, count=gm.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table)

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Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||[ERROR]: M02233_58_000000000-A987R_1_2116_15303_2660M00532_57_000000000-A7L49_1_1117_19528_13608 is not in your count table. Please correct.

2

Hi Ann,
I pulled down your fasta file and you have 440,918 unique sequences. Your distance matrix must be huge. I suspect that caused a merging error and the count table mismatch, but I don’t think it would have been able to cluster anyway. Pat recently wrote a blog to address this common question we get, http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/.
Kindly,
Sarah