Error "pick_de_novo_otus.py" for oomycetes

[Alberto Rojas]

Hi every one,

I'm working currently in oomycetes microbial diversity, but when I run the command: pick_de_novo_otus.py

This error appear:

Stderr

Error in assign_taxonomy.py: Option --id_to_taxonomy_fp is required when assigning with uclust.

I don't have a good experience about this, so I'll be grateful for your help!

Cheers!!!

[Jose]

Hi Alberto,

the error message indicates you need to provide a taxonomy file for you to run this command. This happens during the call to assign_taxonomy.py that pick_de_novo_otus.py makes. If you are using Greengenes, this file will be called something like:

/path/to/greengenes/taxonomy/97_otu_taxonomy.txt

where "/path/to/greengenes" should be replaced by the actual location of Greengenes. In order to pass this file to pick_de_novo_otus.py you need to specify it in a parameters file passed through the --parameter_fp option:

pick_de_novo_otus.py -i seqs.fna -o output_dir --parameter_fp params.txt

the format of params.txt is explained here:

http://qiime.org/documentation/qiime_parameters_files.html

Jose