Hello mothur forums
Just ran my first MiSeq data through the pipeline using your SOP and a freshly compiled 64-bit linux mothur 1.31.2.
I submit here the difference in output between classify.otu with and without basis=sequence parameter:
mothur > classify.otu(list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, label=0.03)
taxlevel rankID taxon daughterlevels total GroupA GroupB GroupC GroupD
0 0 Root 1 10189 3244 2925 2139 2613
1 0.1 Bacteria 7 10189 3244 2925 2139 2613
2 0.1.1 "Actinobacteria" 1 17 1 6 8 8
3 0.1.1.1 Actinobacteria 3 17 1 6 8 8
4 0.1.1.1.1 Bifidobacteriales 1 9 0 4 4 5
5 0.1.1.1.1.1 Bifidobacteriaceae 2 9 0 4 4 5
6 0.1.1.1.1.1.1 Bifidobacterium 0 2 0 1 1 1
6 0.1.1.1.1.1.2 unclassified 0 7 0 3 3 4
4 0.1.1.1.2 Coriobacteriales 1 7 1 2 3 3
mothur > classify.otu(list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, label=0.03, basis=sequence)
head stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.tax.summary
taxlevel rankID taxon daughterlevels total GroupA GroupB GroupC GroupD
0 0 Root 1 -989412472 1265255570 910390184 593052351 536856719
1 0.1 Bacteria 7 -989412472 1265255570 910390184 593052351 536856719
2 0.1.1 "Actinobacteria" 1 217 1 132 51 33
3 0.1.1.1 Actinobacteria 3 217 1 132 51 33
4 0.1.1.1.1 Bifidobacteriales 1 148 0 130 7 11
5 0.1.1.1.1.1 Bifidobacteriaceae 2 148 0 130 7 11
6 0.1.1.1.1.1.1 Bifidobacterium 0 10 0 3 3 4
At first I thought this could be an overflowed signed int. But stability.trim.contigs.fasta only contains 534659 sequences. So I am really in the dark as to what might be happening. Let me know what else you need to see if this is code-bug or user-error. This run was with only 4 of the 192 fastq files I need to process.