[Bio-Linux] Qiime

[Alec Colebrook-Clark]

Hi Tim,

I've just had a person mention that the dependencies for qiime 1.8 are throwing out some errors (shown below).

 qiime > print_qiime_config.py -t
System information
==================
Platform:    linux2
Python version:    2.7.3 (default, Feb 27 2014, 19:58:35) [GCC 4.6.3]
Python executable:    /usr/bin/python

Dependency versions
===================
PyCogent version:    1.5.3
NumPy version:    1.6.1
matplotlib version:    1.1.1rc
biom-format version:    1.1.2
qcli version:    0.1.0
QIIME library version:    1.8.0
QIIME script version:    1.8.0-1biolinux1
PyNAST version (if installed):    1.2.2
Emperor version:    0.9.3
RDP Classifier version (if installed):    rdp_classifier.jar
Java version (if installed):    1.7.0_55

QIIME config values
===================
blastmat_dir:    /usr/share/ncbi/data
jobs_to_start:    1
pynast_template_alignment_blastdb:    None
qiime_scripts_dir:    /usr/lib/qiime/bin/
template_alignment_lanemask_fp:    /usr/share/qiime/data/lanemask_in_1s_and_0s
working_dir:    .
pynast_template_alignment_fp:    /usr/share/qiime/data/core_set_aligned.fasta.imputed
python_exe_fp:    python
temp_dir:    /tmp
blastall_fp:    blastall
seconds_to_sleep:    60
cluster_jobs_fp:    None
F..............F....F.......FF...F.
======================================================================
FAIL: test_FastTree_supported_version (__main__.QIIMEDependencyFull)
FastTree is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/qiime/bin/print_qiime_config.py", line 364, in test_FastTree_supported_version
% ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported FastTree version. 2.1.3 is required, but running 2.1.7.

======================================================================
FAIL: test_gdata_install (__main__.QIIMEDependencyFull)
gdata is installed
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/qiime/bin/print_qiime_config.py", line 754, in test_gdata_install
self.assertTrue(pass_test, "gdata is not installed.")
AssertionError: gdata is not installed.

======================================================================
FAIL: test_pplacer_supported_version (__main__.QIIMEDependencyFull)
pplacer is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/qiime/bin/print_qiime_config.py", line 655, in test_pplacer_supported_version
"which components of QIIME you plan to use.")
AssertionError: pplacer not found. This may or may not be a problem depending on which components of QIIME you plan to use.

======================================================================
FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull)
rtax is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/qiime/bin/print_qiime_config.py", line 634, in test_rtax_supported_version
"which components of QIIME you plan to use.")
AssertionError: rtax not found. This may or may not be a problem depending on which components of QIIME you plan to use.

======================================================================
FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull)
sourcetracker is installed
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/qiime/bin/print_qiime_config.py", line 421, in test_sourcetracker_installed
("SOURCETRACKER_PATH is not set. This is "
AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker.

======================================================================
FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)
usearch is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/qiime/bin/print_qiime_config.py", line 714, in test_usearch_supported_version
% ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) is required, but running
USEARCH is not freely redistributable and is thus not included in the
default QIIME package.
You may obtain a personal copy of the 32-bit program at no charge.

To use this feature, please go to:
http://www.drive5.com/usearch/download.html

Download USEARCH v5.2.236, then:
sudo mv usearch* /usr/local/bin/usearch
sudo chmod a+x /usr/local/bin/usearch

You probably also want to install USEARCH 6.1 as /usr/local/bin/usearch61

.

----------------------------------------------------------------------
Ran 35 tests in 0.221s

FAILED (failures=6)


As far as I know qiime has always been maintained via the apt-get command. Are other users seeing the same errors? I am particularly puzzled by fasttree. Will qiime 1.8 work with fast tree 2.1.7 but throw the error in the qiimw config test?

Thanks
Alec
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