Question: Import_biom with tree problem
0
gravatar for andrebolerbarros
12 months ago by
andrebolerbarros10 wrote:

Hey!

I'm trying to import my mothur data in phyloseq, by first of all import the list, group and tree files:

   phyl<-import_mothur(mothur_list_file = "total.final.pick.opti_mcc.list", mothur_group_file="total.final.pick.groups", mothur_tree_file = "total.final.pick.tre")

However, I get an error message:

`Error in 3:as.integer(rawlines[2]) :

NA/NaN argument In addition:

Warning messages:

1: In asMethod(object) : NAs introduced by coercion

2: In import_mothur_otulist(mothur_list_file, cutoff) : NAs introduced by coercion`

Apparently, there's a problem with the group file, since I can't really import it whatsoever (gives that error message). So, I've tried with import_biom:

   phyl<-import_biom(BIOMfilename = "total.final.pick.opti_mcc.0.03.biom", treefilename = "total.final.pick.tre")

Which, in turn, gives the error output:

`Error in validObject(.Object):

invalid class “phyloseq” object: Component taxa/OTU names do not match.

Taxa indices are critical to analysis. Try taxa_names()`

Is there any suggestion about importing mothur files "directly from the pipeline?

Note: I've seen post suggestion using different tree-producing softwares, but those also require several modifications of the trees. I would like to know if there's a more straightforward solution

phyloseq 16s mothur • 233 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by andrebolerbarros10

Solved in phyloseq github; Issue #408:
Removing the label-row from list file solved the problem

ADD REPLYlink written 12 months ago by andrebolerbarros10
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