Error during creation of filter has me baffled!! Help?!

Commands in mothur
1

Hi!
I’m attempting to align some OTU’s with Blast sequences to make a phylogentic tree. The coding I use is as follows:

mothur > align.seqs(fasta=betaproteo.fasta, reference=silva.bacteria.fasta, flip=t, processors=2)

Using 2 processors.

Reading in the silva.bacteria.fasta template sequences… DONE.
It took 107 to read 14956 sequences.
Aligning sequences from betaproteo.fasta …

Reading in the silva.bacteria.fasta template sequences… DONE.
It took 1520 to read 14956 sequences.
It took 1731 secs to align 55 sequences.


Output File Names: betaproteo.align betaproteo.align.report
mothur > summary.seqs(fasta=betaproteo.align)

Using 2 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1044 22583 389 0 4 1
2.5%-tile: 1044 25300 391 0 4 2
25%-tile: 1044 31144 694 0 5 14
Median: 1132 42545 1097 0 5 28
75%-tile: 13133 43026 1416 0 6 42
97.5%-tile: 15644 43116 1472 1 6 54
Maximum: 15644 43116 1474 1 7 55
Mean: 5354.22 37495.5 1019.51 0.0545455 5.4

of Seqs: 55

Output File Names:
betaproteo.summary

mothur > screen.seqs(fasta=betaproteo.align, optimize=start, criteria=95, end=43026, processors=2)

Using 2 processors.
Optimizing start to 15644.

Output File Names:
betaproteo.good.align
betaproteo.bad.accnos


It took 0 secs to screen 55 sequences.

mothur > filter.seqs(fasta=betaproteo.good.align, vertical=t, trump=., processors=2)

Using 2 processors.
Creating Filter…
Error in reading your fastafile, at position -1. Blank name.

I simply cannot figure out what I’m doing wrong… where on earth is position -1 on a fasta file??
Any help would be hugely appreciated - I only started with mothur a few days ago, so I’m still a newbie!

2

Welcome to the mothur community! It usually means mothur has hit the end of file. Looking at your screen.seqs command, you probably removed most of the 55 sequences you had. The end parameter removes all sequences that end before 43026. Have you looked in the file to see what the sequences look like?