Create OTU table using dist.seqs and cluster Error

Commands in mothur
1

Dear community,
What I have is a fasta file with very similar sequences. From that I created a name file using list.seqs and a dist.file using dist. seqs with no cutoff.
Now I wanted to cluster but get always errors stating that some sequences are not in the name file. But when I look at the names file, I can see that they are there.

mothur > cluster(column=LD12_BG_839seqs.dist,name=LD12_BG_839seqs.accnos)

********************###########
Reading matrix: ||ABError: Sequence ‘EU800141’ was not found in the names file, please correct

Do you have any idea what could be wrong here?
Thanks for you help

2

LD12_BG_839seqs.accnos isn’t a names file. Can you tell/show us how you got these files?

Pat

3

starting point was a fasta file:
fasta=LD12_BG_839seqs.fna

that was the way I tried to go

align.seqs(reference=core_set_aligned.imputed.fasta, processors=2)
list.seqs(fasta=LD12_BG_839seqs.align)
dist.seqs(fasta=LD12_BG_839seqs.align, processors=2)
list.seqs(fasta=LD12_BG_839seqs.align)
cluster(column=LD12_BG_839seqs.dist,name=LD12_BG_839seqs.accnos)

thanks

4

So an accnos file is not the same as a names file. A names file would have been created if you ran unique.seqs and/or pre.cluster. FWIW, you’re really skipping over a few critical steps like generating a group file (trim.seqs), making sure things line up in the same alignment space (screen.seqs), making sure things only overlap the same alignment space (filter.seqs), chimera checking (chimera.uchime). You should really look at our SOPs and get a sense of how your data might fit in.

Pat