problem with trim.seqs command

Commands in mothur
1

Hi There,
i just had a doubt regarding the trim.seqs command. When I try to use to start analyzing my data. When I type this:
trim.seqs(fasta=sample.fna, oligos=sample.oligos, qfile=sample.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=2)
I get the following error: You have 223893 sequences in your fasta file, but 633071 sequences in your quality file.

My first option was to use sffinfo with the original sff file, which I have, but after sffinfo(sff=HZSC42M02.sff, flow=T), I get the following error:
[WARNING]: Your sff file may be corrupted! Sequence:
Clip Qual Left = 5, but we only read 1 bases.
Clip Qual Right = 1280, but we only read 1 bases.

What can be happening here?

Thank you very much for your help

Manuel Aira

2

Sounds like there’s a problem with your sff file - can you get a “fresh” copy from your sequence provider?

3

I am sorry but I cannot understand what means “fresh”
The provider upload the files ( .sff, .fna and .qual) to our ftp 2 times, and I got the same errors all the time.

Thank you very much for your help and fast response

Regards,

Manuel Aira

4

Not sure what to tell you. Sounds like their version of the sff file is corrupted too.

5

Thank you very much for your help. I will talk with the sequence provider in order to know if there was any problem during the 454 run.

Regards,

Manuel Aira