trying to run QIIME in cluster

[Juan Gabriel Giarrizzo]

Hello guys,
I am trying to run the tutorial in my university cluster.
QIIME was not installed by me but by the biocomputing center and I have the suspicios that some dependecies are missing?
Anyway this is the sterror I get when running pick_otus.py
Traceback (most recent call last):
  File "/local/cluster/bin/pick_otus.py", line 593, in <module>
    main()
  File "/local/cluster/bin/pick_otus.py", line 476, in main
    result_path=result_path,log_path=log_path,HALT_EXEC=False)
  File "/local/cluster/lib/python2.7/qiime/pick_otus.py", line 881, in __call__
    HALT_EXEC=HALT_EXEC)
  File "/local/cluster/lib/python2.7/qiime/pycogent_backports/uclust.py", line 550, in get_clusters_from_fasta_filepath
    raise ApplicationError, ('Error running uclust. Possible causes are '
cogent.app.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided

And this is the configuration print out of the qiime intalled in the cluster

System information
==================
         Platform:    linux2
   Python version:    2.7 (r27, Aug 20 2012, 14:38:18)  [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)]
Python executable:    /local/cluster/bin/python2.7

Dependency versions
===================
                     PyCogent version:    1.5.1
                        NumPy version:    1.5.1
                   matplotlib version:    Not installed.
                  biom-format version:    0.9.3
                QIIME library version:    1.5.0-dev
                 QIIME script version:    1.5.0-dev
        PyNAST version (if installed):    Not installed.
RDP Classifier version (if installed):    Not installed.

QIIME config values
===================
blastmat_dir:    None
sc_queue:    all.q
topiaryexplorer_project_dir:    None
pynast_template_alignment_fp:    None
cluster_jobs_fp:    None
pynast_template_alignment_blastdb:    None
assign_taxonomy_reference_seqs_fp:    None
torque_queue:    friendlyq
qiime_test_data_dir:    None
template_alignment_lanemask_fp:    None
 jobs_to_start:    1
cloud_environment:    False
qiime_scripts_dir:    None
denoiser_min_per_core:    50
working_dir:    None
 python_exe_fp:    python
temp_dir:    /tmp/
blastall_fp:    blastall
 seconds_to_sleep:    2
assign_taxonomy_id_to_taxonomy_fp:    None

I am just trying to make sense to te people helping me to be able to run QIIME in the university.
Any suggestions??

Thank you very much


--
Juan Giarrizzo, PhD
Post Doctoral Fellow
Oregon State University
859 4620543 (cell)

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[Yoshiki Vázquez Baeza]

Hello Juan,

Can you run: 

print_qiime_config.py -t 

And:

which uclust

uclust --version

Then send us the output for these commands.

Thanks!

Yoshiki.

--
 
 
 

[Juan Gabriel Giarrizzo]

Thank you Yoshiki,
Attached you will find the txt with the stout of the test with 20 failures
and uclust is nowhere to be found.
So I am guessing my theory could be right?

--
 
 
 

[Yoshiki Vázquez Baeza]

Hello Juan,

Yes some of the dependencies are missing, uclust being one that you specifically need for the command you are trying to run. You might try asking the system admins to install it system wide (which is probably better on the long run), or you can just download the binary and add it to your path.

To download uclust go to this site and select the according version the OS in the cluster of your university: 

http://www.drive5.com/uclust/downloads1_2_22q.html

Once you have the file, rename the file to uclust, then create a directory where you want this binary to live, let's say qiime_sw in your home directory and after that, add that path to your PATH environment variable, like this:

mv uclustq1.2.22_i86linux64 uclust

mkdir ~/qiime_sw/

echo "export PATH=${HOME}/qiime_sw/:\$PATH" >> ~/.bashrc

Open a new terminal and then try:

uclust --version 

Let us know how it goes.

Thanks!

Yoshiki.

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<qiimetest912.txt>