screen command

Hi Everyone,
I am trying to run filter command
filter.seqs(fasta=…/demultiplexed.unique.align)
I am getting an error:
Using 6 processors.
Creating Filter…
Sequences are not all the same length, please correct.
Sequences are not all the same length, please correct.
Sequences are not all the same length, please correct.
Sequences are not all the same length, please correct.
Sequences are not all the same length, please correct.
Sequences are not all the same length, please correct.
The I looked into my summary file which looks like this:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 5 4 0 1 1
2.5%-tile: 439 590 151 0 3 194
25%-tile: 480 630 151 0 4 1933
Median: 498 648 151 0 4 3865
75%-tile: 513 663 151 0 5 5797
97.5%-tile: 545 695 151 0 6 7535
Maximum: 1757 1760 151 0 9 7728
Mean: 496.161 645.85 150.528 0 4.41097

of Seqs: 7728

To overcome the problem I tried using screen seq command which is:
screen.seqs(fasta=…/demultiplexed.unique.align, start=480, end=695)
When I run this I get empty file for good aligns.
Please can anyone explain what is going wrong.

Thanks!!!

What is the exact command text you are using to generate demultiplexed.unique.align?

Thanks Dr. Schloss,
This is the command I am using to get unique sequences:
unique.seqs(fasta=…/demultiplexed.fna)
and this for aligning:
align.seqs(fasta=…/demultiplexed.unique.fna, reference=…/silva.bacteria/silva.bacteria.fasta, flip=T, processors=5)

Thanks Dr. Schloss,
This is the command I am using to get unique sequences:
unique.seqs(fasta=…/demultiplexed.fna)
and this for aligning:
align.seqs(fasta=…/demultiplexed.unique.fna, reference=…/silva.bacteria/silva.bacteria.fasta, flip=T, processors=5)

Thanks!!!

For the screen.seqs command, the start parameter will remove all sequences that start after the position given. The end parameter will remove all sequence that end before the position given. I think you want start=545, end=590.