[Bio-linux-dev] qiime
Mike Cox
mikeyj.cox at gmail.com
Tue Sep 20 12:26:25 EDT 2011
I should add that for some reason, when remotely logging in using FreeNX,
for some reason the terminal won't source that .profile properly and you
have to explicitly source it with:
source .profile
before it starts to play ball. This isn't true when logging in at the
machine itself.
Cheers
Mike
On Wed, Sep 7, 2011 at 23:31, Tony Travis <a.travis at abdn.ac.uk> 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<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)
>>
>
>
> --
> Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
> and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
> tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
> mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.**sari.ac.uk<http://bioinformatics.rri.sari.ac.uk>
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>
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