qiime tests: scripts failed

[Samuel Major]

Hello Again Qiime Masters!

Things have been going well! I got my data loaded, I can see it, it looks like everything is up to date. So I ran a few scripts 

count_seqs.py -i combined_seqs.fna

UnicodeDecodeError: 'utf8' codec can't decode byte 0x9c in position 42: invalid start byte

This is where it got fun. I got to learn a lot about unix and QIIME. Any way, I loaded the source code and ran tests.

It shows that several tests failed, it looks like it's because I'm missing several packages, and 16 commands failed. I think I downloaded all the package correctly(extracted files to the QIIME home file). But the above error occured. I'm also getting a bunch of other fun errors popping up with some other commands. Let me know if these errors might help diagnose and alleviate the problem. THANKS!

################PYTHON TESTS#################

cd qiime-1.9.1/tests

 

python all_tests.py

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

Result summary

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

 

Unit test result summary

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

 

 

Failed the following unit tests.

/home/qiime/qiime-1.9.1/tests/test_parallel/test_assign_taxonomy.py

/home/qiime/qiime-1.9.1/tests/test_parallel/test_map_reads_to_reference.py

/home/qiime/qiime-1.9.1/tests/test_pick_otus.py

 

Failed the following unit tests, in part or whole due to missing external applications.

Depending on the QIIME features you plan to use, this may not be critical.

/home/qiime/qiime-1.9.1/tests/test_assign_taxonomy.py

/home/qiime/qiime-1.9.1/tests/test_identify_chimeric_seqs.py

/home/qiime/qiime-1.9.1/tests/test_make_per_library_sff.py

/home/qiime/qiime-1.9.1/tests/test_map_reads_to_reference.py

/home/qiime/qiime-1.9.1/tests/test_trim_sff_primers.py

/home/qiime/qiime-1.9.1/tests/test_workflow/test_pick_open_reference_otus.py

/home/qiime/qiime-1.9.1/tests/test_workflow/test_upstream.py

 

Script usage test result summary

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

 

Ran 337 commands to test 132 scripts. 16 of these commands failed and 0 scripts could not be tested due to errors.

Failed scripts were: assign_taxonomy.py identify_chimeric_seqs.py map_reads_to_reference.py parallel_assign_taxonomy_rdp.py parallel_map_reads_to_reference.py parallel_pick_otus_usearch61_ref.py pick_closed_reference_otus.py pick_open_reference_otus.py pick_otus.py start_parallel_jobs_torque.py

[Colin Brislawn]

Hello Samuel,

Thanks for posting the test results for us! The new version of qiime comes with another test script, which could be helpful here. Could you try running, 

print_qiime_config.py -t

Thanks! 

Colin 

[Samuel Major]

Thanks,

I ran print_qiime_config.py -t

System information

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

         Platform:   linux2

   Python version:   2.7.3 (default, Jun 22 2015, 19:33:41)  [GCC 4.6.3]

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/0.1.2

 

Dependency versions

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

          QIIME library version:     1.9.1

           QIIME script version:     1.9.1

qiime-default-reference version:     0.1.2

                  NumPy version:     1.9.2

                  SciPy version:     0.15.1

                 pandas version:     0.16.1

             matplotlib version:     1.4.3

            biom-format version:     2.1.4

                   h5py version:     2.4.0 (HDF5 version: 1.8.4)

                   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 [May 26 2015 13:50:14]

                          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:   /qiime_software/blast-2.2.22-release/data

      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:   /qiime_software/blast-2.2.22-release/bin/blastall

                 seconds_to_sleep:   1

 

QIIME base install test results

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

.........

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

Ran 9 tests in 0.026s

 

OK

[TonyWalters]

Samuel, see this thread: https://groups.google.com/forum/#!searchin/qiime-forum/UnicodeDecodeError/qiime-forum/W6NqdoWhNfI/2cYXXYB1UvcJ
You've probably got non-ascii characters in your fasta labels.