Aw: Re: QIIME 1.7 - any users in debian-testing/unstable ?

To: "Simon Kainz" <simon@familiekainz.at>
Cc: "Debian Med Project List" <debian-med@lists.debian.org>
Subject: Aw: Re: QIIME 1.7 - any users in debian-testing/unstable ?
From: "Steffen Möller" <steffen_moeller@gmx.de>
Date: Thu, 28 Nov 2013 20:24:56 +0100 (CET)
Message-id: <[🔎] trinity-45ffaca5-1be7-4619-956e-df91cb463f0c-1385666696204@3capp-gmx-bs28>
In-reply-to: <[🔎] 52973F9A.5050306@familiekainz.at>
References: <[🔎] trinity-afc84424-2111-45a2-97fd-d71180dd01f6-1385555612474@3capp-gmx-bs17>, <[🔎] 52973F9A.5050306@familiekainz.at>

Hi Simon,

Hi Simon,

> We also run (well, i *installed* it for some users) qiime
> 1.7.0+dfsg-1 from unstable. So i could also eventually try to run some
> tests. So contact me, just in case i should try out something.

I suggest you try the lines below.

Best,

Steffen

 
$ apt-get source qiime
$ sudo apt-get install qiime
$ cd qiime-1.7.0+dfsg/tests/
$ ./all_tests.py


In no particular order
 * ApplicationNotFoundError: Cannot find blat. Is it installed? Is it in your path?
 * 
 ======================================================================
ERROR: test_call_infernal_test1 (__main__.InfernalAlignerTests)
InfernalAligner: functions as expected when returing objects
----------------------------------------------------------------------

 *

Testing /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_alpha_diversity.py:

/usr/lib/python2.7/dist-packages/cogent/util/progress_display.py:28: UserWarning: Not using MPI as mpi4py not found
  from cogent.util import parallel, terminal

 * Testing /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_assign_taxonomy.py:

test_call_alt_input_types (__main__.BlastTaxonAssignerTests)
BlastTaxonAssigner.__call__ functions w alt input types ... ERROR
test_call_existing_blast_db (__main__.BlastTaxonAssignerTests)
BlastTaxonAssigner.__call__ functions w existing db ... ERROR
test_call_logs_run (__main__.BlastTaxonAssignerTests)
BlastTaxonAssigner.__call__ logs the run when expected ... ERROR
test_call_on_the_fly_blast_db (__main__.BlastTaxonAssignerTests)
BlastTaxonAssigner.__call__ functions w creating blast db ... ERROR
test_call_output_to_file (__main__.BlastTaxonAssignerTests)
BlastTaxonAssigner.__call__ functions w output to file ... ERROR
ERROR
test_get_blast_hits (__main__.BlastTaxonAssignerTests)
BlastTaxonAssigner._get_blast_hits functions w existing db ... ERROR
test_get_first_blast_hit_per_seq (__main__.BlastTaxonAssignerTests)
Extracting the first blast hit for each seq functions as expected ... ok
test_init (__main__.BlastTaxonAssignerTests)


 * RuntimeError: BLAST cannot run if the BLASTMAT environment variable is not set.

Usually, the BLASTMAT environment variable points to the NCBI data directory,
which contains matrices like PAM30 and PAM70, etc.

Alternatively, you may create a .ncbirc file to define these variables.


 * ApplicationNotFoundError: Cannot find mothur. Is it installed? Is it in your path?

 * ======================================================================
ERROR: test_call_result_to_file (__main__.RdpTaxonAssignerTests)
RdpTaxonAssigner should save results to file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_assign_taxonomy.py", line 850, in test_call_result_to_file
    log_path=None)
  File "/usr/lib/python2.7/dist-packages/qiime/assign_taxonomy.py", line 447, in __call__
    max_memory=max_memory, fixrank=fix_ranks, tmp_dir=tmp_dir)
  File "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/rdp_classifier.py", line 394, in assign_taxonomy
    app = RdpClassifier(**app_kwargs)
  File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 165, in __init__
    self._error_on_missing_application(params)
  File "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/rdp_classifier.py", line 141, in _error_on_missing_application
    "JAR file not found in current directory and the RDP_JAR_PATH "
ApplicationNotFoundError: JAR file not found in current directory and the RDP_JAR_PATH environment variable is not set.  Please set RDP_JAR_PATH to the full pathname of the JAR file.


 * 
======================================================================
ERROR: test_call_paired_result (__main__.RtaxTaxonAssignerTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_assign_taxonomy.py", line 449, in test_call_paired_result
    actual = p(self.input_seqs_fp)
  File "/usr/lib/python2.7/dist-packages/qiime/assign_taxonomy.py", line 748, in __call__
    log_path=log_path,base_tmp_dir=get_qiime_temp_dir())
  File "/usr/lib/python2.7/dist-packages/cogent/app/rtax.py", line 239, in assign_taxonomy
    app_result = app()
  File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 251, in __call__
    open(errfile).read())
ApplicationError: Unacceptable application exit status: 127
Command:
cd "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/"; rtax -a "/tmp/RtaxTaxonAssignerTests_MDgLQe2McLs9Ot4pN314.fasta" -b "/tmp/RtaxTaxonAssignerTests_kyEYQV06DwNu0ZFZgeTc.fasta" -m "/tmp/rtax_GBTCHi2iW0iZQGIBZNy5" -l "/tmp/rtax_GBTCHi2iW0iZQGIBZNy5/ampliconIdsToClassify" -o "/tmp/RtaxAssignments_2jFt94.txt" -i '\S+\s+(\S+?)\/' -t "/tmp/RtaxTaxonAssignerTests_gWd250r71OsFfVONnP1r.txt" -r "/tmp/RtaxTaxonAssignerTests_7O10fQ04as0vKxnVtI0i.fasta" > "/tmp/tmpubkVBs7fhz6anXxcuKy0.txt" 2> "/tmp/tmph1t4yHEzQtkzK40X6Ppq.txt"
StdOut:

StdErr:
sh: 1: rtax: Permission denied


 * ======================================================================
ERROR: test_compare_categories_categorical_variables (__main__.CompareCategoriesTests)
Test compare_categories() on categorical methods/input.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_compare_categories.py", line 89, in test_compare_categories_categorical_variables
    self.cat_categories, self.num_perms, self.test_dir)
  File "/usr/lib/python2.7/dist-packages/qiime/compare_categories.py", line 130, in compare_categories
    rex(command_args, '%s.r' % method, output_dir=out_dir)
  File "/usr/lib/python2.7/dist-packages/qiime/util.py", line 1948, in __call__
    outfile = open(outfilepath,'w')
IOError: [Errno 13] Permission denied: '/tmp/R.stdout'

 * submit_jobs executes commands on the cluster ... ERROR

======================================================================
ERROR: test_adjust_workers (__main__.TestUtils)
adjust_workers stops clients
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_denoiser/test_cluster_util.py", line 126, in test_adjust_workers
    workers, client_sockets = self._setup_server_and_clients()
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_denoiser/test_cluster_util.py", line 89, in _setup_server_and_clients
    verbose=False)
  File "/usr/lib/python2.7/dist-packages/qiime/denoiser/cluster_utils.py", line 93, in setup_workers
    submit_jobs([cmd], tmpname)
  File "/usr/lib/python2.7/dist-packages/qiime/denoiser/cluster_utils.py", line 37, in submit_jobs
    raise ApplicationNotFoundError,"cluster_jobs_fp not set in config file!"

 * ======================================================================
FAIL: test_denoiser_min_per_core (__main__.DenoiserTests)
denoiser_min_per_core is set to a good value
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_denoiser/test_settings.py", line 52, in test_denoiser_min_per_core
    self.fail('denoiser_min_per_core not defined in qiime_config.')
AssertionError: denoiser_min_per_core not defined in qiime_config.

 * ERROR: test_store_cluster (__main__.TestUtils)
store_clusters stores the centroid seqs for each cluster.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_denoiser/test_utils.py", line 115, in test_store_cluster
    store_clusters({}, self.tiny_test, self.tmpdir)
  File "/usr/lib/python2.7/dist-packages/qiime/denoiser/utils.py", line 202, in store_clusters
    (flowgrams, header) = lazy_parse_sff_handle(open(sff_fp))
IOError: [Errno 2] No such file or directory: '/usr/lib/qiime/support_files/denoiser/TestData/tiny_test.sff.txt'

----------------------------------------------------------------------
Ran 18 tests in 0.014s

  * Library optparse not found.

To install: open R and run the command "install.packages("optparse")".

If you already have the optparse package installed in a local directory,
  

 .... more ....

Reply to:

References:
- QIIME 1.7 - any users in debian-testing/unstable ?
  - From: "Steffen Möller" <steffen_moeller@gmx.de>
- Re: QIIME 1.7 - any users in debian-testing/unstable ?
  - From: Simon Kainz <simon@familiekainz.at>

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