mothur > get.lineage(constaxonomy=run066_09122016.an.cons.pick.taxonomy, list=run066_09122016.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list, taxon=Bacteria;"Proteobacteria";Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;, label=0.03)
taxonomy looks like this:
OTU Size
Taxonomy Otu000001
981823 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(100);
Otu000002 368600
Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Sphingomonadales(100);Sphingomonadaceae(100);Sphingomonas(100); Otu000003
330772 Bacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Oxalobacteraceae(100);
Otu000004 288861
Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(100);
Is the taxon format wrong? Because there is no output and the command never finishes…
I don’t remember taking it very long with remove.lineage(taxon=choroplast-mitochondria) and there was 30-40% seq contamination.
There seems to be something wrong with the run066_09122016.an.cons.pick.taxonomy file, which was generated from run066_09122016.an.cons.taxonomy after I removed some taxon before (have to look it up), but it’s certainly a file which mothur produced. The formatting seems to be off, because when I look at the precursor taxonomy file:
OTU Size Taxonomy
Otu000001 981823 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(100);
Otu000002 368600 Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Sphingomonadales(100);Sphingomonadaceae(100);Sphingomonas(100);
Otu000003 330772 Bacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Oxalobacteraceae(100);
Otu000004 288861 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(100);
Otu000005 273636 Bacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(98);
Otu000006 217047 Bacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Oxalobacteraceae(100);Massilia(72);
Otu000007 201452 Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Sphingomonadales(100);Sphingomonadaceae(100);Sphingomonas(100)
seems like the file format was somehow broken? I don’t know why.
So I used the precursor taxonomy file instead with the same command:
get.lineage(constaxonomy=run066_09122016.an.cons.taxonomy, list=run066_09122016.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list, taxon=Bacteria;"Proteobacteria";Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;, label=0.03)
Your taxonomy file does not contain any OTUs from Bacteria;"Proteobacteria";Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;.
Your file does not contain OTUs from Bacteria;"Proteobacteria";Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;.
Selected 0 OTUs from your list file.
but the taxon format is wrong? In the SOP, you use the same format for the taxon parameter. Could it be the quotes on Proteobacteria? But that’s just how it’s listed in the taxonomy file.
So I changed taxon to just “Pseudomonas”:
get.lineage(constaxonomy=run066_09122016.an.cons.taxonomy, list=run066_09122016.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list, taxon=Pseudomonas, label=0.03)Selected 338 OTUs from your list file.
Output File Names:
run066_09122016.an.cons.pick.taxonomy
run066_09122016.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.0.03.pick.list
this worked finally.
It’s still a mistery to me why the taxonomy file format was somehow broken…