mothur analysis pipeline script

trim.seqs(fasta=CN.fa,qfile=CN.quala, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=7)
system(./grupp_CN.pl CN.trim.fasta > CN.groups)
unique.seqs(fasta=CN.trim.fasta)
align.seqs(fasta=CN.trim.unique.fasta, reference=gg.ref.fasta, processors=7,flip=T)
summary.seqs(fasta=CN.trim.unique.align)
screen.seqs(fasta=CN.trim.unique.align, name=CN.trim.names, group=CN.groups, end=4951,start=4655,minlength=65,processors=7)
summary.seqs(fasta=current)
filter.seqs(fasta=CN.trim.unique.good.align, vertical=T, trump=., processors=7)
unique.seqs(fasta=CN.trim.unique.good.filter.fasta, name=CN.trim.good.names)
pre.cluster(fasta=CN.trim.unique.good.filter.unique.fasta, name=CN.trim.unique.good.filter.names, group=CN.good.groups, diffs=1)
chimera.uchime(fasta=CN.trim.unique.good.filter.unique.precluster.fasta, name=CN.trim.unique.good.filter.unique.precluster.names, group=CN.good.groups, processors=7)
remove.seqs(accnos=CN.trim.unique.good.filter.unique.precluster.uchime.accnos, fasta=CN.trim.unique.good.filter.unique.precluster.fasta, name=CN.trim.unique.good.filter.unique.precluster.names, group=CN.good.groups)
system(mv CN.trim.unique.good.filter.unique.precluster.pick.names CN.final.names)
system(mv CN.trim.unique.good.filter.unique.precluster.pick.fasta CN.final.fasta)
system(mv CN.good.pick.groups CN.final.groups)
system(./gr_puhas CN.final.groups > CN.proovikaupa.groups)
remove.groups(fasta=CN.final.fasta, name=CN.final.names, group=CN.proovikaupa.groups, groups=11A-13A-11B-13B)
classify.seqs(fasta=CN.final.pick.fasta,template=gg_99.pds.ng.fasta, taxonomy=gg_99.pds.tax, cutoff=80, processors=7, method=knn)
remove.lineage(taxonomy=CN.final.pick.pds.taxonomy, name=CN.final.pick.names, group=CN.proovikaupa.pick.groups, fasta=CN.final.pick.fasta, taxon=k__Archaea;unclassified;-k__Bacteria;unclassified;, dups=T)
system(mv CN.final.pick.pick.names CNP.final.names)
system(mv CN.final.pick.pick.fasta CNP.final.fasta)
system(mv CN.proovikaupa.pick.pick.groups CNP.proovikaupa.groups)
system(mv CN.final.pick.pds.pick.taxonomy CNP.final.taxonomy)
system(./gr_suureks CNP.proovikaupa.groups > CNP.final.groups)
dist.seqs(fasta=CNP.final.fasta, cutoff=0.10, processors=7)
cluster(column=CNP.final.dist, name=CNP.final.names,method=furthest)
make.shared(list=CNP.final.fn.list, group=CNP.proovikaupa.groups, label=0.05)
count.groups()
sub.sample(shared=CNP.final.fn.shared, size=8326)
#everything fine and dandy to this point (only few notifications, at classify.seqs > There are no common levels for sequence #DBNW5DQ1:84:B04B8ABXX:5:1101:10800:19470:1:N:0:_80bp_80.0_0.86_CN_6A. #DBNW5DQ1:84:B04B8ABXX:5:1101:10800:19470:1:N:0:_80bp_80.0_0.86_CN_6A will be #disregarded.)
#Might this be the source of problems?
#Now the next command(classify) will produce these error messages.
#DBNW5DQ1:84:B04B8ABXX:5:1101:10800:19470:1:N:0:_80bp_80.0_0.86_CN_6A is not in your taxonomy file. I will not include it in the consensus.
#Warning: cannot find taxon no_consensus in reference taxonomy tree at level 0. This may cause totals of daughter levels not to add up in summary file.
#DBNW5DQ1:84:B04B8ABXX:5:1101:10800:19470:1:N:0:_80bp_80.0_0.86_CN_6A is represented by #DBNW5DQ1:84:B04B8ABXX:5:1101:9982:18199:1:N:0:_80bp_80.0_0.86_CN_6A #and is not in your taxonomy file. I will not include it in the consensus.
#so yeah this might mbe the source of my problems
classify.otu(list=CNP.final.fn.list, name=CNP.final.names, taxonomy=CNP.final.taxonomy, label=0.05, cutoff=80, reftaxonomy=gg_99.pds.tax)
#next command(make.shared(list=CNP.final.tx.list, group=CNP.proovikaupa.groups, label=1)) will cause error messages like
#[ERROR]: DBNW5DQ1:84:B04B8ABXX:5:2208:9429:200091:1:N:0:_80bp_80.0_0.86_CN_14B is in your groupfile and not your listfile. Please correct.
#Your group file contains 4021388 sequences and list file contains 4020773 sequences. Please correct.
#For a list of names that are in your group file and not in your list file, please refer to CNP.final.tx.missing.name.
#it also seems to hang up(mothur using processor but doesn’t seem to get anywhere for an hour or so, screen stays on the last lines of these notifications
#(please refer to CNP.final.tx.missing.name etc.) though no *missing* or other new files are created.)
#Is it the same problem caused by sequences that were disregarded at the classify.seqs command?
make.shared(list=CNP.final.tx.list, group=CNP.proovikaupa.groups, label=1)