import_biom error - Githubissues

joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

http://joey711.github.io/phyloseq/

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import_biom error #500

Closed DeniRibicic closed 9 years ago

DeniRibicic commented 9 years ago

I have a problem when importing a biom file. I'm always getting the same error message when running this command (no matter what reference database I use in Qiime ):

import_biom(biomfile, treefile, parseFunction = parse_taxonomy_default())

Error:

Error in gsub("^[[:space:]]{1,}", "", char.vec) : argument "char.vec" is missing, with no default

Anyone knows what this means?

Thanks, Deni

joey711 commented 9 years ago

Hard to diagnose without a file.

Can you provide a (preferably small) file that gives that error?
Did you try importing with out providing the other file?
What version of the biom-format is this file?

DeniRibicic commented 9 years ago

Hi again,

I'm actually new to R, the file is big and I don't know how to make it smaller :/. However, when I import just biom file it works!. The biom file was created with Qiime 1.8.0. Anyways, I managed to import all the necessary data with import_qiime command.

Deni

joey711 commented 9 years ago

Great!