I’m having a great time with Mothur, but I can’t figure out what I’m doing wrong here. I’m running the following sequence of commands, but when I get to classify.seqs I get the error:
SAMPLEXXX|1|8250|group-group-group… is not in your name file please correct. When I check the name file SAMPLEXXX is present. Would greatly appreciate any suggestions.
unique.seqs(fasta=all_SAR11.fasta)
align.seqs(candidate=all_SAR11.unique.fasta, template=core_set_aligned.imputed.fasta, ksize=8, align=needleman, gapopen=-2, flip=T, processors=50)
screen.seqs(start=1903, minlength=200, maxambig=0, processors=50, fasta=all_SAR11.unique.align, group=all_SAR11.groups, name=all_SAR11.names)
filter.seqs(fasta=all_SAR11.unique.good.align-core_set_aligned.imputed.fasta, vertical=T, trump=., processors=50)
unique.seqs(fasta=all_SAR11.unique.good.filter.fasta)
pre.cluster(fasta=all_SAR11.unique.good.filter.unique.fasta, name=all_SAR11.unique.good.filter.names)
split.abund(fasta=all_SAR11.unique.good.filter.unique.precluster.fasta, name=all_SAR11.unique.good.filter.unique.precluster.names, cutoff=10)
chimera.slayer(fasta=all_SAR11.unique.good.filter.unique.precluster.rare.fasta, template=core_set_aligned.imputed.filter.fasta, minsnp=100, minbs=100, divergence=1.05, processors=50)
remove.seqs(accnos=all_SAR11.unique.good.filter.unique.precluster.rare.slayer.accnos, fasta=all_SAR11.unique.good.filter.unique.precluster.fasta)
remove.seqs(accnos=all_SAR11.unique.good.filter.unique.precluster.rare.slayer.accnos, name=all_SAR11.unique.good.filter.unique.precluster.names, dups=T)
remove.seqs(accnos=all_SAR11.unique.good.filter.unique.precluster.rare.slayer.accnos, group=all_SAR11.good.groups)
dist.seqs(fasta=all_SAR11.unique.good.filter.unique.precluster.fasta, cutoff=0.20, processors=50)
system(cp all_SAR11.unique.good.filter.unique.precluster.fasta all_SAR11.final.fasta)
system(cp all_SAR11.unique.good.filter.unique.precluster.names all_SAR11.final.names)
system(cp all_SAR11.unique.good.filter.unique.precluster.dist all_SAR11.final.dist)
system(cp all_SAR11.good.groups all_SAR11.final.groups)
read.dist(column=all_SAR11.final.dist, name=all_SAR11.final.names)
cluster()
get.oturep(column=all_SAR11.final.dist, name=all_SAR11.final.names, list=all_SAR11.final.fn.list, fasta=all_SAR11.final.fasta, group=all_SAR11.final.groups, label=0.03)
classify.seqs(fasta=all_SAR11.final.fn.0.03.rep.fasta, template=silva.bacteria_archaea_nitro.rdp.fasta, taxonomy=silva.bacteria_archaea_nitro.rdp.taxonomy, group=all_SAR11.final.groups, name=all_SAR11.final.names, cutoff=60, probs=F, processors=50)
quit()