pick_otus.py uclust issues

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Caitlin Potter

Jan 9, 2016, 8:40:50 AM1/9/16
to Qiime 1 Forum

I am trying to run uclust with pick_otus.py command but have been getting the following error:

Traceback (most recent call last):
  File "/usr/lib/qiime/bin/pick_otus.py", line 999, in <module>
  File "/usr/lib/qiime/bin/pick_otus.py", line 787, in main
    result_path=result_path, log_path=log_path, HALT_EXEC=False)
  File "/usr/lib/python2.7/dist-packages/qiime/pick_otus.py", line 1286, in __call__
  File "/usr/lib/python2.7/dist-packages/bfillings/uclust.py", line 583, in get_clusters_from_fasta_filepath
    raise ApplicationError('Error running uclust. Possible causes are '
burrito.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

However, I have run 'validate_demultiplexed_fasta.py' and found no issues with my input file, and I think my uclust installation is correct:

$  qiime > uclust --version
uclust v1.2.22q
$  qiime > which uclust

I have also tried clustering the reads directly with "usearch -cluster_fast" (32-bit version), and had no issue, which leads me to believe this is not a memory issue (although I could be wrong?). My input fasta file is only 68Mb.

The results of print_qiime_config.py -t are below:

System information
         Platform:    linux2
   Python version:    2.7.6 (default, Mar 22 2014, 22:59:56)  [GCC 4.8.2]
Python executable:    /usr/bin/python

QIIME default reference information
For details on what files are used as QIIME's default references, see here:

Dependency versions
          QIIME library version:    1.9.0
           QIIME script version:    1.9.0+dfsg-0biolinux5
qiime-default-reference version:    0.1.1
                  NumPy version:    1.8.2
                  SciPy version:    0.13.3
                 pandas version:    0.13.1
             matplotlib version:    1.3.1
            biom-format version:    2.1.4
                   h5py version:    2.2.1 (HDF5 version: 1.8.11)
                   qcli version:    0.1.0
                   pyqi version:    0.3.2
             scikit-bio version:    0.2.3
                 PyNAST version:    1.2.2
                Emperor version:    0.9.51
                burrito version:    0.9.0
       burrito-fillings version:    Installed.
              sortmerna version:    SortMeRNA version 2.0, 29/11/2014
              sumaclust version:    SUMACLUST Version 1.0.01
                  swarm version:    Swarm 1.2.20 [Feb  1 2015 09:42:15]
                          gdata:    Not installed.

QIIME config values
For definitions of these settings and to learn how to configure QIIME, see here:

                     blastmat_dir:    /usr/share/ncbi/data
                  cluster_jobs_fp:    None
      pick_otus_reference_seqs_fp:    /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                    jobs_to_start:    1
pynast_template_alignment_blastdb:    None
                qiime_scripts_dir:    /usr/lib/qiime/bin/
                      working_dir:    .
     pynast_template_alignment_fp:    /usr/share/qiime/data/core_set_aligned.fasta.imputed
                    python_exe_fp:    python
                         temp_dir:    /tmp
assign_taxonomy_reference_seqs_fp:    # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
                      blastall_fp:    blastall
                 seconds_to_sleep:    60
assign_taxonomy_id_to_taxonomy_fp:    # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

QIIME base install test results
Ran 9 tests in 0.015s


Apologies for posting when there are a few similar questions here already- however, none of them have helped me solve this issue.

Thanks and best,


Se Jin Song

Jan 11, 2016, 11:10:02 AM1/11/16
to Qiime 1 Forum
Hi Caitlin,

Can you post the results of 
print_qiime_config.py -tf

Se Jin

Caitlin Potter

Jan 11, 2016, 11:54:27 AM1/11/16
to Qiime 1 Forum
Hi Se Jin,

On running 'print_qiime_config.py -tf', it turned out I had the wrong version of usearch installed. I have installed the correct one and it now appears to be working correctly.

Thanks very much for your help!


Se Jin Song

Jan 11, 2016, 1:01:41 PM1/11/16
to Qiime 1 Forum
Glad I could help!
Se Jin
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