RDP classifier

[Carmen Morales]

Hi!


Is there someone around here???

I'm trying to use assign_taxonomy.py with the RDP classifier. I have qiime installed using Miniconda, I downloaded rdp_classifier-2.2.jar but Im not be able to install it or put in the right place to work

Can someone help me?

Thank you

[Greg Caporaso]

Hi Carmen, Can you provide some more detail on the issue that you're running into? Have you followed this step in the documentation? If that step was successful, you should see the path you added in your ~/.bashrc file when you enter the following command:

echo $RDP_JAR_PATH

Best,

Greg

[Carmen Morales]

Hi Greg!

So far I have always worked with BLAST  to assign the taxonomy.

The error I get is : Error in assign_taxonomy.py: Unable to detect RDP Classifier version in file classifier.jar

I tried folllowed the step in the documentation but I dont have or I dont find this $HOME/app/so I dont know where copy the folder with the rdp_classifier_2.2....

If I run     echo $RDP_JAR_PATH  I get /miniconda3/envs/qiime1/bin/rdp_classifier_2.12/dist/classifier.jar

This is my version of qiime:
System information
==================
         Platform:    linux2
   Python version:    2.7.14 |Anaconda, Inc.| (default, Oct 16 2017, 17:29:19)  [GCC 7.2.0]
Python executable:    /home/ga79kev/miniconda3/envs/qiime1/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:    1.13.3
                  SciPy version:    0.19.1
                 pandas version:    0.20.3
             matplotlib version:    1.4.3
            biom-format version:    2.1.5
                   h5py version:    2.7.0 (HDF5 version: 1.10.1)
                   qcli version:    0.1.1
                   pyqi version:    0.3.2
             scikit-bio version:    0.2.3
                 PyNAST version:    1.2.2
                Emperor version:    0.9.51
                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 [Mar  1 2016 23:41:10]
                          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:    /home/ga79kev/miniconda3/envs/qiime1/lib/python2.7/site-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:    /home/ga79kev/miniconda3/envs/qiime1/lib/python2.7/site-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:    /home/ga79kev/miniconda3/envs/qiime1/lib/python2.7/site-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:    /home/ga79kev/miniconda3/envs/qiime1/lib/python2.7/site-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


Thank you

Carmen

[Greg Caporaso]

Hi Carmen,

A couple of things to check. Can you post the output of running the following commands.

First, let's run print_qiime_config.py, but with the -f (full install) flag to see if QIIME is finding the RDP classifier:

print_qiime_config.py -f

And second, let's try just calling RDP classifier outside of QIIME:

jar $RDP_JAR_PATH --help

If you could also run ls on the directory that contains the rdp_classifier-2.2.jar file, that would be helpful. The other RDP classifier files need to be present in that same directory.

For example, my RDP_JAR_PATH is: /Users/gregcaporaso/Applications/rdp_classifier_2.2/rdp_classifier-2.2.jar

If I run ls on the directory containing rdp_classifier-2.2.jar, I see the following files:

$ ls /Users/gregcaporaso/Applications/rdp_classifier_2.2/

COPYRIGHT README docs lib rdp_classifier-2.2.jar sampledata src

If you're not seeing those other files, could you try downloading and unzipping the RDP classifier zip file again? 

Thanks!