rdp classification error

[Salim]

Hi,

I get the following error when I try to run rdp classifier:

assign_taxonomy.py -i rep_set/denoised_seqs_trimmed_rep_set.fasta -o rdp_assigned_taxonomy_silva_c0.8 -t ~/packages/QIIME_files_SILVA104/taxonomy_mapping/Silva_RDP_taxa_mapping.txt -r ~/packages/QIIME_files_SILVA104/rep_set/silva_104_rep_set.fasta

Traceback (most recent call last):

  File "/home/salim/packages/qiime-1.3.0-release/bin/assign_taxonomy.py", line 178, in <module>

    main()

  File "/home/salim/packages/qiime-1.3.0-release/bin/assign_taxonomy.py", line 174, in main

    result_path=result_path,log_path=log_path)

  File "/home/salim/packages/qiime-1.3.0-release/lib/qiime/assign_taxonomy.py", line 386, in __call__

    classification_output_fp=result_path)

  File "/home/salim/packages/pycogent-1.5.1-release/lib/python2.6/site-packages/cogent/app/rdp_classifier.py", line 691, in train_rdp_classifier_and_assign_taxonomy

    training_seqs_file, taxonomy_file, training_dir)

  File "/home/salim/packages/pycogent-1.5.1-release/lib/python2.6/site-packages/cogent/app/rdp_classifier.py", line 663, in train_rdp_classifier

    return app(training_seqs_file)

  File "/home/salim/packages/pycogent-1.5.1-release/lib/python2.6/site-packages/cogent/app/util.py", line 250, in __call__

    % (str(exit_status),command)

cogent.app.util.ApplicationError: Unacceptable application exit status: 1, command: cd "/home/salim/Documents/tmp/otus/"; java -Xmx1000m -cp "/home/salim/packages/rdpclassifier-2.2-release/rdp_classifier-2.2.jar" edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker /tmp/RdpTaxonomy_uYfwqW.txt "/tmp/tmpK6OgqYGAHvTmlh6eZWms.txt" 1 version1 cogent /tmp/RdpTrainer_ljhlUl > "/tmp/tmpCQ0MR0EkSo00tlwOgFlh.txt" 2> "/tmp/tmpcNERop4043yXwcnHkUqk.txt"

What am I doing wrong?

thanks in advance,

Salim

[TonyWalters]

Hello Salim,

Can you run print_qiime_config.py and send me the settings?

Also, when did you download the Silva reference set? There was a
short period, before the QIIME 1.3.0 release, where the taxonomy
mapping was incompatable with RDP 2.2.

-Tony

On Jul 11, 1:01 am, Salim <mjfi2...@gmail.com> wrote:
> Hi,
> I get the following error when I try to run rdp classifier:
>

> *assign_taxonomy.py -i rep_set/denoised_seqs_trimmed_rep_set.fasta -o
> rdp_assigned_taxonomy_silva_c0.8 -t
> ~/packages/QIIME_files_SILVA104/taxonomy_mapping/Silva_RDP_taxa_mapping.txt
> -r ~/packages/QIIME_files_SILVA104/rep_set/silva_104_rep_set.fasta*

> Traceback (most recent call last):
>   File "/home/salim/packages/qiime-1.3.0-release/bin/assign_taxonomy.py",
> line 178, in <module>
>     main()
>   File "/home/salim/packages/qiime-1.3.0-release/bin/assign_taxonomy.py",
> line 174, in main
>     result_path=result_path,log_path=log_path)
>   File
> "/home/salim/packages/qiime-1.3.0-release/lib/qiime/assign_taxonomy.py",
> line 386, in __call__
>     classification_output_fp=result_path)
>   File

> "/home/salim/packages/pycogent-1.5.1-release/lib/python2.6/site-packages/co­gent/app/rdp_classifier.py",

> line 691, in train_rdp_classifier_and_assign_taxonomy
>     training_seqs_file, taxonomy_file, training_dir)
>   File

> "/home/salim/packages/pycogent-1.5.1-release/lib/python2.6/site-packages/co­gent/app/rdp_classifier.py",

> line 663, in train_rdp_classifier
>     return app(training_seqs_file)
>   File

> "/home/salim/packages/pycogent-1.5.1-release/lib/python2.6/site-packages/co­gent/app/util.py",

[Salim Bougouffa]

Hi Tony,

I downloaded the silva reference set today.

As for the config print, I'll email it to you when I arrive in the office first thing in the morning.

Regards,

Salim

[Salim Bougouffa]

Hi Tony,

Follows is the output from print_qiime_config.py -t

System information

==================

         Platform: linux2

   Python version: 2.6.4 (r264:75706, Jul  4 2011, 14:49:50)  [GCC 4.5.2]

Python executable: /home/salim/packages/python-2.6.4-release/bin/python

Dependency versions

===================

                     PyCogent version: 1.5.1

                        NumPy version: 1.3.0

                   matplotlib version: 0.98.5.3

                QIIME library version: 1.3.0

                 QIIME script version: 1.3.0

        PyNAST version (if installed): 1.1

RDP Classifier version (if installed): rdp_classifier-2.2.jar

QIIME config values

===================

                     blastmat_dir: /home/salim/packages/blast-2.2.22-release/data

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /home/salim/packages/core_set_aligned.fasta.imputed

                  cluster_jobs_fp: /home/salim/packages/qiime-1.3.0-release/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb: None

                     torque_queue: friendlyq

   template_alignment_lanemask_fp: /home/salim/packages/lanemask_in_1s_and_0s

                    jobs_to_start: 1

                cloud_environment: False

                qiime_scripts_dir: /home/salim/packages/qiime-1.3.0-release/bin

            denoiser_min_per_core: 50

                      working_dir: /tmp/

                    python_exe_fp: /home/salim/packages/python-2.6.4-release/bin/python

                         temp_dir: /tmp/

                      blastall_fp: /home/salim/packages/blast-2.2.22-release/bin/blastall

                 seconds_to_sleep: 60

running checks:

FastTree is in path and version is supported ... ok

INFERNAL is in path and version is supported ... ok

AmpliconNoise install looks sane. ... FAIL

blast is in path and version is supported ... ok

blastall_fp is set to a valid path ... ok

blastmat_dir is set to a valid path. ... ok

cdbtools is in path and version is supported ... ok

cd-hit is in path and version is supported ... ok

no obvious problems with ChimeraSlayer install ... ok

clearcut is in path and version is supported ... ok

cluster_jobs_fp is set to a valid path and is executable ... ok

denoiser aligner is ready to use ... ok

local qiime_config has no extra params ... ok

maptplotlib version is supported ... ok

mothur is in path and version is supported ... ok

muscle is in path and version is supported ... ok

numpy version is supported ... ok

pynast version is supported ... ok

pynast_template_alignment_blastdb, if set, is set to a valid path ... ok

pynast_template_alignment, if set, is set to a valid path ... ok

python_exe_fp is set to a working python env ... ok

python is in path and version is supported ... ok

qiime_scripts_dir, if set, is set to a valid path ... ok

raxmlHPC is in path and version is supported ... ok

temp_dir, if set, is set to a valid path ... ok

template_alignment_lanemask, if set, is set to a valid path ... ok

uclust is in path and version is supported ... ok

working_dir, if set, is set to a valid path ... ok

======================================================================

FAIL: AmpliconNoise install looks sane.

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

Traceback (most recent call last):

  File "/home/salim/packages/qiime-1.3.0-release/bin/print_qiime_config.py", line 116, in test_ampliconnoise_install

    "$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url)

AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://www.qiime.org/install/install.html#ampliconnoise-install for help.

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

Ran 28 tests in 0.444s

FAILED (failures=1)

Kind regards,

Salim

[TonyWalters]

Hello Salim,

It seems that on certain systems, the default memory allocation for
the RDP classifier of 1000 mb is not quite enough, and is the cause of
this error. Unfortunately, the ability to set the memory usage as a
parameter was only recently implemented, you would need to install the
development version of QIIME and PyCogent to utilize the memory
parameter (using --rdp_max_memory 2000 with assign_taxonomy.py should
work).

The instructions on installing QIIME natively are found here:
http://www.qiime.org/install/install.html#getting-qiime

And for PyCogent:
http://pycogent.sourceforge.net/install.html

Best regards,
Tony Walters

> AssertionError: $PYRO_LOOKUP_FILE variable is not set. Seehttp://www.qiime.org/install/install.html#ampliconnoise-installfor help.

>
> ----------------------------------------------------------------------
> Ran 28 tests in 0.444s
>
> FAILED (failures=1)
>
> Kind regards,
> Salim
>

> On 12 July 2011 01:05, Salim Bougouffa <mjfi2...@gmail.com> wrote:
>
> > Hi Tony,
>
> > I downloaded the silva reference set today.
>
> > As for the config print, I'll email it to you when I arrive in the office
> > first thing in the morning.
>
> > Regards,
> > Salim
>

[Newbie]

Hi Tony,

I was also trying to run assign_taxonomy.py and getting an error. Below is my command and the error message that followed:

qiime@qiime-VirtualBox:~/Desktop/08092012_Rhizobox_Fungal_ITS_Analysis$ assign_taxonomy.py -i '/home/qiime/Desktop/08092012_Rhizobox_Fungal_ITS_Analysis/rep_set.fna' -t '/home/qiime/qiime_software/unite_taxonomy_21nov2011/unite_id_to_taxonomy_map_21nov2011.txt' -r '/home/qiime/qiime_software/unite_taxonomy_21nov2011/unite_ref_seqs_21nov2011.fasta' -o pick_otus/rdp_assigned_taxonomy_unite/ --rdp_max_memory 2000

Traceback (most recent call last):

  File "/home/qiime/qiime_software/qiime-1.5.0-release/bin/assign_taxonomy.py", line 226, in <module>
    main()
  File "/home/qiime/qiime_software/qiime-1.5.0-release/bin/assign_taxonomy.py", line 222, in main
    result_path=result_path,log_path=log_path)
  File "/home/qiime/qiime_software/qiime-1.5.0-release/lib/qiime/assign_taxonomy.py", line 364, in __call__
    max_memory=max_memory)
  File "/home/qiime/qiime_software/qiime-1.5.0-release/lib/qiime/pycogent_backports/rdp_classifier.py", line 492, in train_rdp_classifier_and_assign_taxonomy
    training_seqs_file, taxonomy_file, training_dir, max_memory=max_memory)
  File "/home/qiime/qiime_software/qiime-1.5.0-release/lib/qiime/pycogent_backports/rdp_classifier.py", line 464, in train_rdp_classifier
    return app(training_seqs_file)
  File "/home/qiime/qiime_software/qiime-1.5.0-release/lib/qiime/pycogent_backports/rdp_classifier.py", line 320, in __call__
    result = super(RdpClassifier, self).__call__(data=data, remove_tmp=remove_tmp)
  File "/home/qiime/qiime_software/pycogent-1.5.1-release/lib/python2.7/site-packages/cogent/app/util.py", line 250, in __call__
    % (str(exit_status),command)
cogent.app.util.ApplicationError: Unacceptable application exit status: 1, command: cd "/home/qiime/Desktop/08092012_Rhizobox_Fungal_ITS_Analysis/"; java -Xmx2000M -cp "/home/qiime/qiime_software/rdpclassifier-2.2-release/rdp_classifier-2.2.jar" edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker "/tmp/RdpTaxonomy_ortdzN.txt" "/tmp/tmpKWgspPGsWhDDRPeVRARC.txt" 1 version1 cogent "/tmp/RdpTrainer_6LwCeg" > "/tmp/tmpxpOL2agYItetMf2cgUqi.txt" 2> "/tmp/tmp0dEsG6IsrXxL39nnE6Pt.txt"

Any idea what I am doing wrong? This is with --rdp_max_memory 2000.

Thank you in advance,
Molli

[Tony Walters]

Hello Molli,

You need a lot of memory specified with --rdp_max_memory and the default UNITE taxonomy mapping file (--rdp_max_memory 12000).  I created an alternative taxonomy mapping file that you can download in this thread here (https://groups.google.com/group/qiime-forum/browse_thread/thread/f73d5325b0e1a1bd/bb2f13af39b82e25?lnk=gst&q=unite+memory#bb2f13af39b82e25) which you can use with --rdp_max_memory 4000.

-Tony

--
 
 
 

[Molli Newman]

Thanks so much, Tony!  I will try it out and let you know how it works. BTW, all of you who manage this forum and respond so clearly are lifesavers! Thank you!

 

Molli

 

Post-Doctoral Fellow

Department of Entomology and Plant Pathology

209 Rouse Life Sciences Building

Auburn University

Auburn, AL 36849 USA

www.wix.com/ramsemm/newman

--
 
 
 

[Newbie]

Worked perfectly! Thank you, Tony!

Molli