[Bio-Linux] Problem Calling ChimeraSlayer through Qiime installed on Bio-Linux 6
Anat Eck
anate25 at gmail.com
Fri Nov 4 12:32:03 EDT 2011
Dear Bio-Linux users,
I'm trying to run ChimeraSlayer using Qiime 1.3.0 on Bio-Linux.
The versions I have installed are:
dpkg -s qiime bio-linux-qiime chimeraslayer | grep ^Version
Version: 1.3.0-0ubuntu6
Version: 1:1.3.0bl-6
Version: 20101212-1ubuntu5
I have ChimeraSlayer in the PATH, but for some reason I get an error when
trying to call it using the qiime script as follows:
identify_chimeric_seqs.py -i rep_set_aligned.fna -a
Silva_108_core_aligned_seqs.fna -o chimeric_seqs.txtTraceback (most recent
call last):
File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 172, in <module>
main()
File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 169, in main
keep_intermediates=keep_intermediates)
File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 148, in chimeraSlayer_identify_chimeras
keep_intermediates=keep_intermediates):
File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 133, in __call__
keep_intermediates=keep_intermediates)
File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 592, in get_chimeras_from_Nast_aligned
app_results = app()
File "/usr/lib/pymodules/python2.6/cogent/app/util.py", line 269, in
__call__
result_paths=self._get_result_paths(data))
File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 405, in _get_result_paths
raise ApplicationError,"Calling ChimeraSlayer failed."
cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.
I will be grateful for a hint if this kind of error had occurred to anyone
else.
I'm attaching the configuration report I get from Qiime:
root at chaysavanh-desktop:~# 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): Not installed.
QIIME config values
===================
blastmat_dir: /usr/share/ncbi/data
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: None
cluster_jobs_fp: None
pynast_template_alignment_blastdb: None
torque_queue: friendlyq
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. ... ok
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 ... ok
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 ... ok
local qiime_config has no extra params ... ok
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: 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: 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: 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 0.048s
FAILED (failures=5, errors=1)
And my PATH value:
root at chaysavanh-desktop:~# grep -i chimera ~/.bashrc
/root/.bashrc:export
PATH=:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/NX/bin:/usr/lib/qiime/bin:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer
Thank you,
Anat
2011/11/4 Tim Booth via RT <website at nebc.nerc.ac.uk>
> Hi Anat,
>
> I think you just need to run:
>
> sudo apt-get install bio-linux-qiime
>
> This is a wrapper package that, amongst othter things, installs the
> uCLust clustering tool. We can't put that in the main package due to
> licensing restrictions.
>
> Cheers,
>
> TIM
>
>
> --
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>
>
>
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