When I using the taxonomy filie “ssu_ref_102_tax_slv.txt” which was downloaded from Silva website, the programme shutdown automated.
The command is :
mothur> clasiffy.seqs(fasta=mysequence.fasta, template=SSURef_102_tax_silva.fasta, taxomony=ssu_ref_102_tax_slv.txt)
Does anyone konws what is the problem ? or
Where can i get the taxonomy file form website?
Is the file in the correct format? I seem to remember that those files have spaces and maybe slashes. Spaces in names (e.g. Escherichia et rel) need to be changed to underscores (e.g. Escherichia_et_rel) and slashes or what ever separates the various levels needs to be replaced with semicolons. It’s also entirely possible that your template file is not properly formatted. You can get both at http://www.mothur.org/wiki/Taxonomy_outline