Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
65 lines (52 sloc) 3.13 KB
#!bash
module load basemount
PROJECTNAME=$1
basemount ../basemountpoint/basespace
# The way that our server handles mounting permissions, I have to change my whole home dir to 777 before mounting
#chmod 777 /YOURHOMEDIR
mkdir -p $PROJECTNAME/fastq
for f in basespace/Projects/$PROJECTNAME/Samples/*/Files/*.gz;
do s=${f##basespace/Projects/$PROJECTNAME/Samples/}; s=${s%%/*};
cp $f $PROJECTNAME"/fastq/"$s"."${f##*Files/};
done
# unmount then change permissions back to 700
#basemount --unmount /YOURHOMEDIR/basemountpoint/basespace
#chmod 700 /YOURHOMEDIR
cd $PROJECTNAME
mv fastq/fileList.paired.file $PROJECTNAME.file
module load mothur/1.38.1
mothur "#make.file(inputdir=fastq, type=gz);"
module load mothur/1.39.4
mothur "#make.contigs(file=$PROJECTNAME.file);
make.contigs(processors=32, file=current);
summary.seqs(fasta=current);
screen.seqs(fasta=current, group=current, summary=current, maxambig=0, maxlength=275);
summary.seqs(fasta=current);
unique.seqs(fasta=current);
summary.seqs(fasta=current, name=current);
count.seqs(name=current, group=current);
align.seqs(fasta=current, reference=silva.nr_v119.v4.align);
summary.seqs(fasta=current, count=current);
screen.seqs(fasta=current, count=current, summary=current, start=1968, end=11550, maxhomop=8);
filter.seqs(fasta=current, vertical=T);
summary.seqs(fasta=current, count=current);
pre.cluster(fasta=current, diffs=2, count=current);
summary.seqs(fasta=current, count=current);
chimera.vsearch(fasta=current, count=current, dereplicate=t);
remove.seqs(fasta=current, accnos=current, count=current);
summary.seqs(fasta=current, count=current);
classify.seqs(fasta=current, count=current, reference=silva.nr_v119.v4.align, taxonomy=silva.nr_v119.tax, cutoff=80);
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota);
summary.tax(taxonomy=current, count=current);
dist.seqs(fasta=current, countends=F, cutoff= 0.03, processors=16);
cluster(column=current, count=current, method=opti);
summary.seqs(processors=32);
make.shared(list=current, count=current);
classify.otu(list=current, count=current, taxonomy=current);
get.oturep(fasta=current, count=current, list=current, method=abundance);
count.groups(shared=current);
summary.single(shared=current, calc=nseqs-sobs-coverage-shannon-shannoneven-invsimpson, subsample=10000);
dist.shared(shared=current, calc=braycurtis-jest-thetayc, subsample=10000);
sub.sample(taxonomy=$PROJECTNAME.trim.contigs.good.unique.good.filter.precluster.pick.nr_v119.wang.pick.taxonomy, count=$PROJECTNAME.trim.contigs.good.unique.good.filter.precluster.denovo.vsearch.pick.pick.pick.count_table, list=$PROJECTNAME.trim.contigs.good.unique.good.filter.precluster.pick.pick.opti_mcc.list, size=10000, persample=true, label=0.03);
summary.tax(taxonomy=current, count=current);
system(mkdir send); system(cp *shared send); system(cp *cons.tax* send); system(cp *pick.tax.summary send); system(cp *pick.subsample.tax.summary send); system(cp *.rep.fasta send); system(cp *lt.ave.dist send); system(cp *groups.ave-std.summary send); system(cp mothur.batch send); system(cp mothur.*.logfile send);"
You can’t perform that action at this time.