Created
February 1, 2013 11:17
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maasha@maxwell:~/data/qiime_tutorial-v1.5.0$ 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/QIIME1.6/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/QIIME1.6/bin/start_parallel_jobs.py | |
pynast_template_alignment_blastdb: /home/maasha/install/QIIME1.6/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/QIIME1.6/data/lanemask_in_1s_and_0s | |
jobs_to_start: 24 | |
cloud_environment: False | |
qiime_scripts_dir: /home/maasha/Install/QIIME1.6/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 ... ok | |
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 ... ok | |
test_working_dir (__main__.Qiime_config) | |
working_dir, if set, is set to a valid path ... ok | |
---------------------------------------------------------------------- | |
Ran 35 tests in 2.847s | |
OK |
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