gistfile1.txt

maasha@orsted:~$ print_qiime_config.py -t

System information
==================
         Platform:      linux2
   Python version:      2.7.3 (default, Jan 28 2013, 09:50:08)  [GCC 4.4.5]
Python executable:      /disk/orsted/install/maasha/QIIME1.6/bin/python

Dependency versions
===================
                     PyCogent version:  1.5.3
                        NumPy version:  1.5.1
                   matplotlib version:  1.1.0
                  biom-format version:  1.1.1
                QIIME library version:  1.6.0
                 QIIME script version:  1.6.0
        PyNAST version (if installed):  1.2
RDP Classifier version (if installed):  rdp_classifier-2.2.jar
          Java version (if installed):  1.6.0_18

QIIME config values
===================
                     blastmat_dir:      /home/maasha/install/QIIME/src/blast/data
                         sc_queue:      all.q
      topiaryexplorer_project_dir:      None
     pynast_template_alignment_fp:      /home/maasha/install/QIIME1.6/data/gg_12_10_otus/rep_set/97_otus.fasta
                  cluster_jobs_fp:      /home/maasha/Install/QIIME/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb:      /home/maasha/install/QIIME/data/core_set_aligned.fasta.imputed
assign_taxonomy_reference_seqs_fp:      None
                     torque_queue:      friendlyq
              qiime_test_data_dir:      None
   template_alignment_lanemask_fp:      /home/maasha/install/QIIME/data/lanemask_in_1s_and_0s
                    jobs_to_start:      10
                cloud_environment:      False
                qiime_scripts_dir:      /home/maasha/Install/QIIME/bin
            denoiser_min_per_core:      50
                      working_dir:      None
                    python_exe_fp:      python
                         temp_dir:      /tmp
                      blastall_fp:      blastall
                 seconds_to_sleep:      60
assign_taxonomy_id_to_taxonomy_fp:      None


running checks:

test_FastTree_supported_version (__main__.Qiime_config)
FastTree is in path and version is supported ... ok
test_INFERNAL_supported_version (__main__.Qiime_config)
INFERNAL is in path and version is supported ... ok
test_ParsInsert_supported_version (__main__.Qiime_config)
ParsInsert is in path and version is supported ... ok
test_R_supported_version (__main__.Qiime_config)
R is in path and version is supported ... ok
test_ampliconnoise_install (__main__.Qiime_config)
AmpliconNoise install looks sane. ... ok
test_blast_supported_version (__main__.Qiime_config)
blast is in path and version is supported ... ok
test_blastall_fp (__main__.Qiime_config)
blastall_fp is set to a valid path ... ok
test_blastmat_dir (__main__.Qiime_config)
blastmat_dir is set to a valid path. ... ok
test_cdbtools_supported_version (__main__.Qiime_config)
cdbtools is in path and version is supported ... ok
test_cdhit_supported_version (__main__.Qiime_config)
cd-hit is in path and version is supported ... ok
test_chimeraSlayer_install (__main__.Qiime_config)
no obvious problems with ChimeraSlayer install ... ok
test_clearcut_supported_version (__main__.Qiime_config)
clearcut is in path and version is supported ... ok
test_cluster_jobs_fp (__main__.Qiime_config)
cluster_jobs_fp is set to a valid path and is executable ... ok
test_denoiser_supported_version (__main__.Qiime_config)
denoiser aligner is ready to use ... FAIL
test_for_obsolete_values (__main__.Qiime_config)
local qiime_config has no extra params ... ok
test_gdata_install (__main__.Qiime_config)
gdata is installed ... ok
test_matplotlib_suported_version (__main__.Qiime_config)
maptplotlib version is supported ... ok
test_mothur_supported_version (__main__.Qiime_config)
mothur is in path and version is supported ... ok
test_muscle_supported_version (__main__.Qiime_config)
muscle is in path and version is supported ... ok
test_numpy_suported_version (__main__.Qiime_config)
numpy version is supported ... ok
test_pplacer_supported_version (__main__.Qiime_config)
pplacer is in path and version is supported ... ok
test_pynast_suported_version (__main__.Qiime_config)
pynast version is supported ... ok
test_pynast_template_alignment_blastdb_fp (__main__.Qiime_config)
pynast_template_alignment_blastdb, if set, is set to a valid path ... ok
test_pynast_template_alignment_fp (__main__.Qiime_config)
pynast_template_alignment, if set, is set to a valid path ... ok
test_python_exe_fp (__main__.Qiime_config)
python_exe_fp is set to a working python env ... ok
test_python_supported_version (__main__.Qiime_config)
python is in path and version is supported ... ok
test_qiime_scripts_dir (__main__.Qiime_config)
qiime_scripts_dir, if set, is set to a valid path ... ok
test_qiime_test_data_dir (__main__.Qiime_config)
qiime_test_data_dir, if set, is set to a valid path ... ok
test_raxmlHPC_supported_version (__main__.Qiime_config)
raxmlHPC is in path and version is supported ... ok
test_rtax_supported_version (__main__.Qiime_config)
rtax is in path and version is supported ... ok
test_temp_dir (__main__.Qiime_config)
temp_dir, if set, is set to a valid path ... ok
test_template_alignment_lanemask_fp (__main__.Qiime_config)
template_alignment_lanemask, if set, is set to a valid path ... ok
test_uclust_supported_version (__main__.Qiime_config)
uclust is in path and version is supported ... ok
test_usearch_supported_version (__main__.Qiime_config)
usearch is in path and version is supported ... FAIL
test_working_dir (__main__.Qiime_config)
working_dir, if set, is set to a valid path ... ok

======================================================================
FAIL: test_denoiser_supported_version (__main__.Qiime_config)
denoiser aligner is ready to use
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maasha/install/QIIME1.6/bin/print_qiime_config.py", line 538, in test_denoiser_supported_version
    "which components of QIIME you plan to use.")
AssertionError: Denoiser flowgram aligner not found or not executable.This may or may not be a problem depending on which components of QIIME you plan to use.

======================================================================
FAIL: test_usearch_supported_version (__main__.Qiime_config)
usearch is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maasha/install/QIIME1.6/bin/print_qiime_config.py", line 688, in test_usearch_supported_version
    % ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) is required, but running 5.2.32
.

----------------------------------------------------------------------
Ran 35 tests in 0.506s

FAILED (failures=2)