### Iceland2014-current-4proc.batch
### 2015-02-12 01

### Process the silva data.  
### trim inputted sequences to start and end specifications, do not keep unknown bases
system(/bin/echo  "starting silva pcr.seqs `date`" >>/dev/stderr)
pcr.seqs(fasta=silva.bacteria.fasta, start=13862, end=23444, keepdots=F)
system(mv silva.bacteria.pcr.fasta silva.v4.fasta)
system(/bin/ls -ltr > mothur-output-files-0.txt)

### Summary of the silva data.
system(/bin/echo  "starting silva summary.seqs `date`" >>/dev/stderr)
summary.seqs(fasta=silva.v4.fasta)
system(/bin/ls -ltr > mothur-output-files-1.txt)

system(/bin/echo  "starting  make.contigs `date`" >>/dev/stderr)
make.contigs(file=Iceland2014.files, processors=2)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-2.txt)

system(/bin/echo  "starting  screen.seqs `date`" >>/dev/stderr)
screen.seqs(fasta=current, group=current, summary=current, maxambig=0, maxlength=275)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-3.txt)

system(/bin/echo  "starting  unique.seqs `date`" >>/dev/stderr)
unique.seqs(fasta=current)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-4.txt)

system(/bin/echo  "starting  count.seqs `date`" >>/dev/stderr)
count.seqs(name=current, group=current)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-5.txt)

system(/bin/echo  "starting  align.seqs `date`" >>/dev/stderr)
align.seqs(fasta=current, reference=silva.v4.fasta)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-6.txt)

system(/bin/echo  "starting  screen.seqs `date`" >>/dev/stderr)
screen.seqs(fasta=current, count=current, start=8, end=9582, maxhomop=8)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-7.txt)

system(/bin/echo  "starting  filter.seqs `date`" >>/dev/stderr)
filter.seqs(fasta=current, vertical=T, trump=.)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-8.txt)

system(/bin/echo  "starting  unique.seqs `date`" >>/dev/stderr)
unique.seqs(fasta=current, count=current)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-9.txt)

system(/bin/echo  "starting  pre.cluster `date`" >>/dev/stderr)
pre.cluster(fasta=current, count=current, diffs=2)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-10.txt)

system(/bin/echo  "starting  chimera.uchime `date`" >>/dev/stderr)
chimera.uchime(fasta=current, count=current, dereplicate=t)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-11.txt)

system(/bin/echo  "starting  remove.seqs `date`" >>/dev/stderr)
remove.seqs(fasta=current, accnos=current)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-12.txt)

system(/bin/echo  "starting  classify.seqs `date`" >>/dev/stderr)
classify.seqs(fasta=current, count=current, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-13.txt)

system(/bin/echo  "starting  remove.lineage `date`" >>/dev/stderr)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-14.txt)

system(/bin/echo  "starting  cluster.split `date`" >>/dev/stderr)
cluster.split(fasta=current,count=current, taxonomy=current, splitmethod=classify, taxlevel=4,large=T, cutoff=0.15)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-15.txt)

system(/bin/echo  "starting  make.shared `date`" >>/dev/stderr)
make.shared(list=current, count=current, label=0.03)
summary.seqs(fasta=current)
system(/bin/ls -ltr > mothur-output-files-16.txt)

quit()
        
#classify.otu(list=Iceland2014.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list, count=Iceland2014.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, taxonomy=Iceland2014.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, label=0.03)