Aug 4 11:41 unix306 bar_exedMISEQ0714% print_qiime_config.py -t System information ================== Platform: linux2 Python version: 2.7 (r27:82500, Sep 12 2010, 22:20:51) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] Python executable: /usr/local/bioinf/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/0.1.3 Dependency versions =================== QIIME library version: 1.9.1-dev QIIME script version: 1.9.1-dev qiime-default-reference version: 0.1.3 NumPy version: 1.11.1 SciPy version: 0.17.1 pandas version: 0.16.0 matplotlib version: 1.3.1 biom-format version: 2.1.5 h5py version: 2.5.0 (HDF5 version: 1.8.14) 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 [Jul 21 2016 16:10:28] 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: /usr/local/bioinfsoftware/qiime/current/qiime-deploy/qiime_software/blast-2.2.22-release/data pick_otus_reference_seqs_fp: /usr/local/bioinfsoftware/python/current/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta python_exe_fp: python sc_queue: all.q topiaryexplorer_project_dir: None pynast_template_alignment_fp: /usr/local/bioinfsoftware/qiime/current/qiime-deploy/qiime_software/core_set_aligned.fasta.imputed cluster_jobs_fp: /usr/local/bioinfsoftware/qiime/src/Qiime/scripts/start_parallel_jobs.py pynast_template_alignment_blastdb: None assign_taxonomy_reference_seqs_fp: /usr/local/bioinfsoftware/qiime/current/qiime-deploy/qiime_software/gg_otus-13_8-release/rep_set/97_otus.fasta torque_queue: friendlyq template_alignment_lanemask_fp: /usr/local/bioinfsoftware/qiime/current/qiime-deploy/qiime_software/lanemask_in_1s_and_0s jobs_to_start: 4 slurm_time: None cloud_environment: False qiime_scripts_dir: /usr/local/bioinfsoftware/qiime/src/Qiime/scripts denoiser_min_per_core: 50 working_dir: /home/users/allstaff/penington.j/.TemporaryItems assign_taxonomy_id_to_taxonomy_fp: /usr/local/bioinfsoftware/qiime/current/qiime-deploy/qiime_software/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt temp_dir: /home/users/allstaff/penington.j/.TemporaryItems/ slurm_memory: None slurm_queue: None blastall_fp: blastall seconds_to_sleep: 2 QIIME base install test results =============================== ...F..... ====================================================================== FAIL: test_for_unrecognized_values (__main__.QIIMEDependencyBase) qiime_config has no extra values ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/bioinfsoftware/python/current/bin/print_qiime_config.py", line 313, in test_for_unrecognized_values error_msg_fragment % ", ".join(extra_vals)) AssertionError: The .qiime_config in your HOME contains unrecognized values: cloud_environment, qiime_scripts_dir, template_alignment_lanemask_fp, working_dir, python_exe_fp You can safely remove these values from your QIIME config file as they will be ignored by QIIME. ---------------------------------------------------------------------- Ran 9 tests in 0.241s FAILED (failures=1)