Dear Forum,
I’m trying to update my batch file with the new silva files announced today on mothur.org. Below is my batch file. The first thing I’m asking for help with is making sure I’m using the correct silva files in the correct commands. The second issue I’m having is that I can run commands successfully all the way to make.shared(list=current, group=current, count=current, label=0.03). After trying to run that command, I get an error:
mothur > make.shared(list=current, count=current, label=0.03)
Using colon.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table as input file for the count parameter.
Using colon.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list as input file for the list parameter.
[ERROR]: Your count file does not have group info, aborting.
[ERROR]: did not complete make.shared.
Does anyone have suggestions on how to resolve? This batch file was working fine until I tried updating it for the new silva files.
pcr.seqs(fasta=silva.nr_v128.align, start=11894, end=25319, keepdots=F, processors=8) system(mv silva.nr_v128.pcr.align silva.v128.fasta)
#change the name of the file from colon.files to whatever suits the study make.contigs(file=colon.files, processors=16) summary.seqs(fasta=colon.trim.contigs.fasta) screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275) unique.seqs(fasta=current) count.seqs(name=current, group=current) summary.seqs(count=colon.trim.contigs.good.count_table) align.seqs(fasta=current, reference=silva.v128.fasta, flip=t) summary.seqs(fasta=colon.trim.contigs.good.unique.align, count=colon.trim.contigs.good.count_table) screen.seqs(fasta=current, count=current, start=1968, end=11550, maxhomop=8) summary.seqs(fasta=current, count=current) filter.seqs(fasta=current, vertical=T, trump=.) unique.seqs(fasta=current, count=current) summary.seqs(fasta=current, count=current) pre.cluster(fasta=current, count=current, diffs=3) chimera.uchime(fasta=current, count=current, dereplicate=t) remove.seqs(fasta=current, accnos=current) summary.seqs(fasta=current, count=current) classify.seqs(fasta=current, count=current, reference=silva.v128.fasta, taxonomy=silva.nr_v128.tax, cutoff=80) remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota) summary.tax(taxonomy=current, count=current) cluster.split(fasta=current, count=current, taxonomy=colon.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v128.wang.taxonomy, splitmethod=classify, taxlevel=6, cutoff=0.2, processors=8) make.shared(list=current, group=current, count=current, label=0.03) classify.otu(list=current, count=current, taxonomy=current, label=0.03) phylotype(taxonomy=current) make.shared(list=current, count=current, group=current, label=1) classify.otu(list=current, count=current, taxonomy=current, label=1) dist.seqs(fasta=current, output=lt, processors=32) system(mv colon.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.shared colon.an.shared) system(mv colon.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.taxonomy colon.an.cons.taxonomy) count.groups(shared=colon.an.shared) sub.sample(shared=colon.an.shared, size=11000) rarefaction.single(shared=colon.an.shared, calc=sobs, freq=100) summary.single(shared=colon.an.shared, calc=nseqs-coverage-sobs-invsimpson-shannon, subsample=11000) heatmap.bin(shared=colon.an.0.03.subsample.shared, scale=log2, numotu=50) dist.shared(shared=colon.an.shared, calc=thetayc-jclass, subsample=11000) heatmap.sim(phylip=colon.an.thetayc.0.03.lt.ave.dist) heatmap.sim(phylip=colon.an.jclass.0.03.lt.ave.dist) tree.shared(phylip=colon.an.thetayc.0.03.lt.ave.dist) parsimony(tree=colon.an.thetayc.0.03.lt.ave.tre, group=mouse.diet.design, groups=all) parsimony(tree=colon.an.thetayc.0.03.lt.ave.tre, group=mouse.treatment.design, groups=all) parsimony(tree=colon.an.thetayc.0.03.lt.ave.tre, group=mouse.sex.design, groups=all) pcoa(phylip=colon.an.thetayc.0.03.lt.ave.dist) nmds(phylip=colon.an.thetayc.0.03.lt.ave.dist) nmds(phylip=colon.an.thetayc.0.03.lt.ave.dist, mindim=3, maxdim=3) amova(phylip=colon.an.thetayc.0.03.lt.ave.dist, design=mouse.diet.design) amova(phylip=colon.an.thetayc.0.03.lt.ave.dist, design=mouse.treatment.design) amova(phylip=colon.an.thetayc.0.03.lt.ave.dist, design=mouse.sex.design) homova(phylip=colon.an.thetayc.0.03.lt.ave.dist, design=mouse.diet.design) homova(phylip=colon.an.thetayc.0.03.lt.ave.dist, design=mouse.treatment.design) homova(phylip=colon.an.thetayc.0.03.lt.ave.dist, design=mouse.sex.design) corr.axes(shared=colon.an.0.03.subsample.shared, axes=colon.an.thetayc.0.03.lt.ave.pcoa.axes) corr.axes(shared=colon.an.0.03.subsample.shared, axes=colon.an.thetayc.0.03.lt.ave.nmds.axes) corr.axes(shared=colon.an.0.03.subsample.shared, axes=colon.an.thetayc.0.03.lt.ave.pcoa.axes, method=spearman, numaxes=3) corr.axes(shared=colon.an.0.03.subsample.shared, axes=colon.an.thetayc.0.03.lt.ave.nmds.axes, method=spearman, numaxes=3) metastats(shared=colon.an.0.03.subsample.shared, design=mouse.diet.design) metastats(shared=colon.an.0.03.subsample.shared, design=mouse.sex.design) metastats(shared=colon.an.0.03.subsample.shared, design=mouse.treatment.design)