Hello!

I followed your examples to the T and thank you so much for the ease of this package. I wanted to know if you came across any of these errors and how I could go about fixing them.

I see that Mothur is in my path, so I don't know why it isn't picking it up. Should I dl these files and install them myself?

FAIL: test_denoiser_supported_version (main.QIIMEDependencyFull)

denoiser aligner is ready to use

Traceback (most recent call last): File "/usr/local/bin/print_qiime_config.py", line 570, in test_denoiser_supported_version "Denoiser flowgram aligner not found or not " 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_h5py (main.QIIMEDependencyFull)

h5py is installed

Traceback (most recent call last): File "/usr/local/bin/print_qiime_config.py", line 709, in test_h5py "h5py is not installed. You should install this for " AssertionError: h5py is not installed. You should install this for improved performance with large BIOM files or if working with BIOM format version 2.x files. For more information, see http://qiime.org/documentation/file_formats.html#biom-file-format-versions

Ran 27 tests in 0.247s

FAILED (failures=3, errors=1)

System information

     Platform:  linux2

Python version: 2.7.6 (default, Nov 2 2015, 15:47:43) [GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] Python executable: /usr/local/bin/python2.7

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
             QIIME script version:  1.9.1
  qiime-default-reference version:  0.1.3
                    NumPy version:  1.10.1
                    SciPy version:  0.16.1
                   pandas version:  0.17.0
               matplotlib version:  1.5.0
              biom-format version:  2.1.5
                     h5py version:  Not installed.
                     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 [Nov  2 2015 16:15:50]
                            gdata:  Installed.

RDP Classifier version (if installed): rdp_classifier-2.2.jar Java version (if installed): 1.6.0_36

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:  /export/apps/qiime/1.8.0/bin/blast-2.2.22-release/data
  pick_otus_reference_seqs_fp:  /usr/local/lib/python2.7/site-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/site-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/site-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/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt temp_dir: /tmp/ slurm_memory: None slurm_queue: None blastall_fp: /export/apps/qiime/1.8.0/bin/blast-2.2.22-release/bin/blastall seconds_to_sleep: 1

QIIME full install test results

...F........F...FE.........

ERROR: test_mothur_supported_version (main.QIIMEDependencyFull)

mothur is in path and version is supported

Traceback (most recent call last): File "/usr/local/bin/print_qiime_config.py", line 549, in test_mothur_supported_version version_string = stdout.strip().split(' ')[1].strip('v.') IndexError: list index out of range

FAIL: test_ampliconnoise_install (main.QIIMEDependencyFull)

AmpliconNoise install looks sane.

Traceback (most recent call last): File "/usr/local/bin/print_qiime_config.py", line 382, in test_ampliconnoise_install "$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url) AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.

qiime / qiime-deploy

A few errors #82