phyloseq and qiime - problem

[Filipa Godoy-Vitorino]

Dear all,

here trying to import qiime data into phyloseq...I get this error on the mapping file...any ideas?

Thx

> qiimedata = import_qiime(otufile, mapfile, trefile, rs_file)

Processing map file...

Error in read.table(file = mapfilename, header = TRUE, sep = "\t", comment.char = "") : 

  no lines available in input

In addition: Warning message:

In file(file, "rt") :

  file("") only supports open = "w+" and open = "w+b": using the former

--

*****
Filipa Godoy-Vitorino, Ph.D.
Assistant Professor and Researcher

PI - Microbial Ecology and Genomics Laboratory (MEGL)

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Inter American University of Puerto Rico Metropolitan Campus

College of Sciences and Technology

Dept. of Natural Sciences

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[jfg]

Hey Fi,

    Ran into this last night too: not sure if you're still stuck but you can work around it by bringing in the mapfile as a separate object and then combining it: 

> mapfile="/home/jfg/jf/sandbox/jf_map.txt"
> map=import_qiime_sample_data(mapfile)
> class(map)
[1] "sample_data"
attr(,"package")
[1] "phyloseq"

> tree=read_tree("/home/jfg/jf/sandbox/otus/rep_OTU_seqs.tre")
> biomfile="/home/jfg/jf/sandbox/otus/otu_table.biom"

> RDEbiom=import_biom(biomfile,parseFunction=parse_taxonomy_default)
> RDE=merge_phyloseq(RDEbiom,tree)

I think it gets you to the same place (though I am combining it with a .biom file; you seem not to be doing that) - good luck.

jfg

[Greg Caporaso]

Hi Fi,

If that doesn't work, you might try posting to the phyloseq issue tracker here. I haven't used phyloseq, so it's hard for me to figure out what might be going wrong, but it does look like it's not able to parse the mapping file. You might want to confirm that the file contents are what you expect by trying to open that file in a text editor. 

Good luck!

Greg