Problems in "align.seqs"

Commands in mothur
1

I had a problem in my Illumina Miseq Sequence data mining with Mothur(my version"Mothur Win").

In the process of picking OTU，I met a error like this “error in reading your fastafile, at position -1. Blank name”
while I was using command line “align.seqs”.

First, my data “stability.trim.contigs.good.unique.fasta” was used to align, I met the error. Then, I download
a 16s rRNA sequence from the NCBI, only including one sequence (about 1500bp). This time, only one
sequence(16s rRNA.fasta) was aligned, the same error came out. The reference file was “silva.
bacteria. fasta”.

I was confused for several days.

2

Can you post the exact syntax of the commands you are running? I’m not clear what you’re doing from you post.

Thanks,
Pat

3

I’ve had this error before and it was because I was using align.seqs with more than one processor, but there was only one sequence to align so the remaining processors could not find anything. This sounds like it is your problem too and can be resolved by reducing processors to 1 for this step.

Cheers
Richard