Hi,
I have a recent sff file generated through V1-4 FLX+ amplicon chemistry from my sequence provider.
Now if I fed it into the initial SOP commands:
sffinfo(sff=sample.sff, flow=T)
trim.flows(flow=sample.flow, oligos=sample.oligos, pdiffs=2, bdiffs=1, minflows=1050, maxflows=1050, order=B, processors=5)
shhh.flows(file=sample.flow.files) <— approximately 11-hours run (lookup file: GS FLX Titanium)
trim.seqs(fasta=sample.shhh.fasta, name=sample.shhh.names, oligo=sample.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, flip=T)
summary.seqs(fasta=sample.shhh.trim.fasta, name=sample.shhh.trim.names)
Plus if I try to proceed further into summary.seqs() here, I get an error prompt mentioning blank input files.
So this left me no choice but to find an alternative quality score approach:
trim.seqs(fasta=sample.fasta, oligos=sample.oligos, qfile=sample.qual, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50) <— “no namefile provided, fasta closely match with name=sample.shhh.trim.names”
summary.seqs(fasta=sample.trim.fasta, name=sample.trim.names)
unique.seqs(fasta=sample.trim.fasta, name=sample.trim.names)
summary.seqs(fasta=sample.trim.unique.fasta, name=sample.trim.unique.names)
align.seqs(fasta=sample.trim.unique.fasta, reference=silva.bacteria.fasta)
summary.seqs(fasta=sample.trim.unique.align, name=sample.trim.unique.names)
screen.seqs(fasta=sample.trim.unique.align, name=sample.shhh.trim.unique.names, group=sample.groups, end=27659, optimize=start, criteria=95)
summary.seqs(fasta=sample.trim.unique.good.align, name=sample.trim.unique.good.names) <— “blank input files, aborting…command not complete”
I just can’t find any solutions here onward (literally buried in a pile of technical problems I know I feel completely unaware of).
Anybody around for a desperate help, please?? 
Daniel