Hi,
I am analyzing a group of 20 related samples.
I get an error when I run make.shared that list file from the classify.seqs can’t be opened.
However when I use the same list file for classify.otu, it works just fine, and the .taxonomy file looks as expected based on the MiSeqSOP.
Anyone know why, or if there is a solution or workaround?
Thanks!
My code and output:
mothur > make.shared(list= seqsElena.trim.contigs.good.good.unique.good.good.flter.unique.precluster.abund.pick.pick.an.unique_list.list, count=seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.uchime.pick.pick.count_table, label=0.03)
Unable to open seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.pick.pick.an.unique_list.list
Using seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.pick.pick.an.unique_list.list as input file for the list parameter.
[ERROR]: did not complete make.shared.
Thanks for the reply Pat,
I ran:
classify.otu(list=seqsElena.trim.contigs.good.good.unique.good.good.flter.unique.precluster.abund.pick.pick.an.unique_list.list, count=seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.uchime.pick.pick.count_table, taxonomy=seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.pick.pds.wang.pick.taxonomy, label=0.03)
The output of
system(ls seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.pick.pick.an.unique_list.list)
is
seqsElena.trim.contigs.good.good.unique.good.good.filter.unique.precluster.abund.pick.pick.an.unique_list.list