add_taxa.py script not found

[Xio Lee]

Hi,

I am trying to add taxonomy table to the OTU table. When I ran add_taxa.py in conda environment, it showed there was no add_taxa.py could be found.

I am wondering where I can get the script and add it to the library?

Thanks,

xio




--------------------------------------------------------------------------------------------------------------------------------------------


System information
==================
         Platform:    linux2
   Python version:    2.7.12 (default, Nov 20 2017, 18:23:56)  [GCC 5.4.0 20160609]
Python executable:    /usr/bin/python

QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
 https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions
===================
          QIIME library version:    1.9.1
           QIIME script version:    1.9.1
qiime-default-reference version:    0.1.3
                  NumPy version:    1.11.0
                  SciPy version:    1.0.0
                 pandas version:    0.21.1
             matplotlib version:    1.5.1
            biom-format version:    2.1.6
                   h5py version:    Not installed.
                   qcli version:    0.1.1
                   pyqi version:    0.3.2
             scikit-bio version:    0.2.3
                 PyNAST version:    1.2.2
                Emperor version:    0.9.60
                burrito version:    0.9.1
       burrito-fillings version:    0.1.1
              sortmerna version:    SortMeRNA version 2.0, 29/11/2014
              sumaclust version:    SUMACLUST Version 1.0.00
                  swarm version:    Swarm 1.2.19 [Dec 14 2017 09:40:14]
                          gdata:    Installed.

QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
 http://qiime.org/install/qiime_config.html
 http://qiime.org/tutorials/parallel_qiime.html

                     blastmat_dir:    None
      pick_otus_reference_seqs_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                         sc_queue:    all.q
      topiaryexplorer_project_dir:    None
     pynast_template_alignment_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
                  cluster_jobs_fp:    start_parallel_jobs.py
pynast_template_alignment_blastdb:    None
assign_taxonomy_reference_seqs_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                     torque_queue:    friendlyq
                    jobs_to_start:    1
                       slurm_time:    None
            denoiser_min_per_core:    50
assign_taxonomy_id_to_taxonomy_fp:    /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                         temp_dir:    /tmp/
                     slurm_memory:    None
                      slurm_queue:    None
                      blastall_fp:    blastall
                 seconds_to_sleep:    1

QIIME base install test results
===============================
.........
----------------------------------------------------------------------
Ran 9 tests in 0.012s

OK

[TonyWalters]

Hello Xio,

Add_taxa.py is a script from a much earlier version of QIIME. See the last example on this page for how to add taxa with biom add-metadata:

http://biom-format.org/documentation/adding_metadata.html

[Xio Lee]

Thanks for the link and update!

Xio