[Bio-linux-dev] qiime
Daniel Pass
daniel.antony.pass at googlemail.com
Wed Sep 21 05:10:25 EDT 2011
Hi all,
Some (although probably not all) of those errors are flagging up because you
need to configure the external programs yourself. Qiime doesn't come with
blast databases built in otherwise it would ramp up the size of the download
and probably be out of date by the time you get it. The default workflow
works fine out of the package that Tim put together but if you want to vary
off the path (ie use Mother or cdhit clustering instead of qiime's favourite
uclust, or blast instead of RDP assignment) then they have given you the
option to point it in the right direction instead of just saying its
impossible.
basically, anything that says "...is in path...FAIL" means you need to have
it configured already on your machine and qiime will use it from there. I
guess from the errors in Tony's post that either blast isn't configured, or
more likely you havent told qiime where to look for it in the
custom_parameters.txt file.
More info on setup here: http://qiime.sourceforge.net/install/install.html
Hope this helps
Dan
On 20 September 2011 17:31, Tim Booth <tbooth at ceh.ac.uk> wrote:
> Hi Tony,
>
> For Qiime, my less-than ideal testing consists of running through the
> tutorial that we use for our Bio-Linux course. Of course, this only
> tests out some of the Qiime features. I've considered working through
> the failures that print_qiime_config.py flags up but what I don't want
> to do is create quick fixes that makes the feature appear to work but
> which are nevertheless untested. Bela, who did the original packaging,
> warned me about this.
>
> So for example if you are trying to use "blast" and can send me a fix
> that both satisfies print_qiime_config.py and also works on your own
> data then I'd be very pleased to incorporate it. Otherwise, I'm only
> fixing these problems as people ask for them specifically. Hopefully at
> some point I'll have the time to go through and do a proper job...
>
> In other news, we should be doing an introductory BL course up in
> Edinburgh on the 4th November, if any Aberdeen people think it is worth
> the trip. I'll send a flyer soon.
>
> Cheers,
>
> TIM
>
> On Wed, 2011-09-07 at 23:31 +0100, Tony Travis wrote:
> > Hi, Tim.
> >
> > I spent today helping my colleague Caroline Reiff try to get "Qiime"
> > working properly under Bio-Linux, and Ubuntu 10.04 LTS with Bio-Linux
> > repositories enabled. There seem to be quite a lot of version conflicts
> > with installed dependencies in your packaged version installed on our
> > Beowulf login server "topcat", and we encountered similar problems on
> > Caroline's workstation, which is Ubuntu 10.04 LTS _ Bio-Linux repo's:
> >
> > Are you working on this already, or should we attempt to fix it?
> >
> > Bye,
> >
> > Tony.
> >
> > > rwt017 at topcat:~$ qiime print_qiime_config.py -t
> > >
> > > System information
> > > ==================
> > > Platform: linux2
> > > Python version: 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC
> 4.4.3]
> > > Python executable: /usr/bin/python2.6
> > >
> > > Dependency versions
> > > ===================
> > > PyCogent version: 1.5.1
> > > NumPy version: 1.3.0
> > > matplotlib version: 0.99.1.1
> > > QIIME library version: 1.3.0
> > > QIIME script version: 1.3.0
> > > PyNAST version (if installed): 1.1
> > > RDP Classifier version (if installed): rdp_classifier-2.0.jar
> > >
> > > QIIME config values
> > > ===================
> > > blastmat_dir: /usr/share/ncbi/data
> > > rdp_classifier_fp: None
> > > topiaryexplorer_project_dir: None
> > > pynast_template_alignment_fp: None
> > > cluster_jobs_fp: None
> > > pynast_template_alignment_blastdb: None
> > > torque_queue: friendlyq
> > > pyronoise_data_fp:
> /usr/local/bioinf/denoiser/denoiser/Data/LookUp.dat
> > > template_alignment_lanemask_fp: None
> > > jobs_to_start: 1
> > > cloud_environment: False
> > > qiime_scripts_dir: /usr/lib/qiime/bin/
> > > denoiser_min_per_core: 50
> > > working_dir: .
> > > python_exe_fp: python
> > > temp_dir: /tmp
> > > blastall_fp: blastall
> > > seconds_to_sleep: 60
> > >
> > >
> > > running checks:
> > >
> > > FastTree is in path and version is supported ... ok
> > > INFERNAL is in path and version is supported ... ok
> > > AmpliconNoise install looks sane. ... FAIL
> > > blast is in path and version is supported ... FAIL
> > > blastall_fp is set to a valid path ... ok
> > > blastmat_dir is set to a valid path. ... ok
> > > cdbtools is in path and version is supported ... ok
> > > cd-hit is in path and version is supported ... ok
> > > no obvious problems with ChimeraSlayer install ... FAIL
> > > clearcut is in path and version is supported ... FAIL
> > > cluster_jobs_fp is set to a valid path and is executable ... ok
> > > denoiser aligner is ready to use ... FAIL
> > > local qiime_config has no extra params ... FAIL
> > > maptplotlib version is supported ... FAIL
> > > mothur is in path and version is supported ... ERROR
> > > muscle is in path and version is supported ... FAIL
> > > numpy version is supported ... ok
> > > pynast version is supported ... ok
> > > pynast_template_alignment_blastdb, if set, is set to a valid path ...
> ok
> > > pynast_template_alignment, if set, is set to a valid path ... ok
> > > python_exe_fp is set to a working python env ... ok
> > > python is in path and version is supported ... ok
> > > qiime_scripts_dir, if set, is set to a valid path ... ok
> > > raxmlHPC is in path and version is supported ... FAIL
> > > temp_dir, if set, is set to a valid path ... ok
> > > template_alignment_lanemask, if set, is set to a valid path ... ok
> > > uclust is in path and version is supported ... ok
> > > working_dir, if set, is set to a valid path ... ok
> > >
> > > ======================================================================
> > > ERROR: mothur is in path and version is supported
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 472, in
> test_mothur_supported_version
> > > version_string = stdout.strip().split(' ')[1].strip('v.')
> > > IndexError: list index out of range
> > >
> > > ======================================================================
> > > FAIL: AmpliconNoise install looks sane.
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 116, 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://www.qiime.org/install/install.html#ampliconnoise-install for help.
> > >
> > > ======================================================================
> > > FAIL: blast is in path and version is supported
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 374, in
> test_blast_supported_version
> > > % ('.'.join(map(str,acceptable_version)), version_string))
> > > AssertionError: Unsupported blast version. 2.2.22 is required, but
> running 2.2.21.
> > >
> > > ======================================================================
> > > FAIL: no obvious problems with ChimeraSlayer install
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 251, in
> test_chimeraSlayer_install
> > > "ChimeraSlayer depends on external files in directoryies relative
> to its "
> > > AssertionError: ChimeraSlayer depends on external files in directoryies
> relative to its install directory. Thesedo not appear to be present.
> > >
> > > ======================================================================
> > > FAIL: clearcut is in path and version is supported
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 525, in
> test_clearcut_supported_version
> > > "which components of QIIME you plan to use.")
> > > AssertionError: clearcut not found. This may or may not be a problem
> depending on which components of QIIME you plan to use.
> > >
> > > ======================================================================
> > > FAIL: denoiser aligner is ready to use
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 497, in
> test_denoiser_supported_version
> > > "which components of QIIME you plan to use.")
> > > 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: local qiime_config has no extra params
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 224, in
> test_for_obsolete_values
> > > ", ".join(extra_vals))
> > > AssertionError: The qiime_config file set via QIIME_CONFIG_FPenviroment
> variable contains obsolete parameters:
> > > rdp_classifier_fp, pyronoise_data_fp
> > >
> > > ======================================================================
> > > FAIL: maptplotlib version is supported
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 332, in
> test_matplotlib_suported_version
> > > version_string))
> > > AssertionError: Unsupported matplotlib version. Must be >= 0.98.5.3 and
> < 0.98.5.4 , but running 0.99.1.1.
> > >
> > > ======================================================================
> > > FAIL: muscle is in path and version is supported
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 458, in
> test_muscle_supported_version
> > > % ('.'.join(map(str,acceptable_version)), version_string))
> > > AssertionError: Unsupported muscle version. 3.6 is required, but
> running 3.7.
> > >
> > > ======================================================================
> > > FAIL: raxmlHPC is in path and version is supported
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > > File "/usr/lib/qiime/bin/print_qiime_config.py", line 504, in
> test_raxmlHPC_supported_version
> > > "which components of QIIME you plan to use.")
> > > AssertionError: raxmlHPC not found. This may or may not be a problem
> depending on which components of QIIME you plan to use.
> > >
> > > ----------------------------------------------------------------------
> > > Ran 28 tests in 0.149s
> > >
> > > FAILED (failures=9, errors=1)
> >
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
> --
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--
Daniel Pass
Tel: (029208)76680
Mob: 07735658687
Room 0.39,
School of Biosciences,
Biological Sciences Building,
Museum Avenue,
Cardiff,
CF10 3AT
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