System information
==================
Platform:
darwin
Python version:
2.7.1 (r271:86832, Dec 15 2011, 08:41:37) [GCC 4.0.1 (Apple Inc. build 5493)]
Python executable:
/macqiime/bin/python
Dependency versions
===================
PyCogent version:
1.5.1
NumPy version:
1.5.1
matplotlib version:
1.1.0
biom-format version:
0.9.3
QIIME library version:
1.5.0
QIIME script version:
1.5.0
PyNAST version (if installed):
1.1
RDP Classifier version (if installed):
rdp_classifier-2.2.jar
QIIME config values
===================
blastmat_dir:
None
sc_queue:
all.q
topiaryexplorer_project_dir:
None
pynast_template_alignment_fp:
/macqiime/greengenes/core_set_aligned.fasta.imputed
cluster_jobs_fp:
/macqiime/QIIME/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb:
None
assign_taxonomy_reference_seqs_fp:
None
torque_queue:
friendlyq
qiime_test_data_dir:
None
template_alignment_lanemask_fp:
/macqiime/greengenes/lanemask_in_1s_and_0s
jobs_to_start:
1
cloud_environment:
False
qiime_scripts_dir:
/macqiime/QIIME/bin/
denoiser_min_per_core:
50
working_dir:
None
python_exe_fp:
/macqiime/bin/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 ... FAIL
test_ampliconnoise_install (__main__.Qiime_config)
AmpliconNoise install looks sane. ... FAIL
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 ... ok
test_for_obsolete_values (__main__.Qiime_config)
local qiime_config has no extra params ... 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_R_supported_version (__main__.Qiime_config)
R is in path and version is supported
----------------------------------------------------------------------