<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>Hi again!<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Also what would be the easiest way to install qiime 1.7? Im trying qiime-deploy but having some difficulty.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Alec<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-language:EN-GB'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-language:EN-GB'> Alec Colebrook-Clark [mailto:aleleb@sahfos.ac.uk] <br><b>Sent:</b> 04 September 2014 10:08<br><b>To:</b> bio-linux@nebclists.nerc.ac.uk<br><b>Subject:</b> [Bio-Linux] Qiime<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>Hi Tim,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>I’ve just had a person mention that the dependencies for qiime 1.8 are throwing out some errors (shown below). <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'><o:p> </o:p></span></p><p class=MsoNormal><span class=apple-converted-space><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'> </span></span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>qiime > print_qiime_config.py -t<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>System information</span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black'><br><span style='background:#FFFFF4'>==================</span><br><span style='background:#FFFFF4'>Platform: linux2</span><br><span style='background:#FFFFF4'>Python version: 2.7.3 (default, Feb 27 2014, 19:58:35) [GCC 4.6.3]</span><br><span style='background:#FFFFF4'>Python executable: /usr/bin/python</span><br><br><span style='background:#FFFFF4'>Dependency versions</span><br><span style='background:#FFFFF4'>===================</span><br><span style='background:#FFFFF4'>PyCogent version: 1.5.3</span><br><span style='background:#FFFFF4'>NumPy version: 1.6.1</span><br><span style='background:#FFFFF4'>matplotlib version: 1.1.1rc</span><br><span style='background:#FFFFF4'>biom-format version: 1.1.2</span><br><span style='background:#FFFFF4'>qcli version: 0.1.0</span><br><span style='background:#FFFFF4'>QIIME library version: 1.8.0</span><br><span style='background:#FFFFF4'>QIIME script version: 1.8.0-1biolinux1</span><br><span style='background:#FFFFF4'>PyNAST version (if installed): 1.2.2</span><br><span style='background:#FFFFF4'>Emperor version: 0.9.3</span><br><span style='background:#FFFFF4'>RDP Classifier version (if installed): rdp_classifier.jar</span><br><span style='background:#FFFFF4'>Java version (if installed): 1.7.0_55</span><br><br><span style='background:#FFFFF4'>QIIME config values</span><br><span style='background:#FFFFF4'>===================</span><br><span style='background:#FFFFF4'>blastmat_dir: /usr/share/ncbi/data</span><br><span style='background:#FFFFF4'>jobs_to_start: 1</span><br><span style='background:#FFFFF4'>pynast_template_alignment_blastdb: None</span><br><span style='background:#FFFFF4'>qiime_scripts_dir: /usr/lib/qiime/bin/</span><br><span style='background:#FFFFF4'>template_alignment_lanemask_fp: /usr/share/qiime/data/lanemask_in_1s_and_0s</span><br><span style='background:#FFFFF4'>working_dir: .</span><br><span style='background:#FFFFF4'>pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed</span><br><span style='background:#FFFFF4'>python_exe_fp: python</span><br><span style='background:#FFFFF4'>temp_dir: /tmp</span><br><span style='background:#FFFFF4'>blastall_fp: blastall</span><br><span style='background:#FFFFF4'>seconds_to_sleep: 60</span><br><span style='background:#FFFFF4'>cluster_jobs_fp: None</span><br><span style='background:#FFFFF4'>F..............F....F.......FF...F.</span><br><span style='background:#FFFFF4'>======================================================================</span><br><span style='background:#FFFFF4'>FAIL: test_FastTree_supported_version (__main__.QIIMEDependencyFull)</span><br><span style='background:#FFFFF4'>FastTree is in path and version is supported</span><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Traceback (most recent call last):</span><br><span style='background:#FFFFF4'>File "/usr/lib/qiime/bin/print_qiime_config.py", line 364, in test_FastTree_supported_version</span><br><span style='background:#FFFFF4'>% ('.'.join(map(str,acceptable_version)), version_string))</span><br><span style='background:#FFFFF4'>AssertionError: Unsupported FastTree version. 2.1.3 is required, but running 2.1.7.</span><br><br><span style='background:#FFFFF4'>======================================================================</span><br><span style='background:#FFFFF4'>FAIL: test_gdata_install (__main__.QIIMEDependencyFull)</span><br><span style='background:#FFFFF4'>gdata is installed</span><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Traceback (most recent call last):</span><br><span style='background:#FFFFF4'>File "/usr/lib/qiime/bin/print_qiime_config.py", line 754, in test_gdata_install</span><br><span style='background:#FFFFF4'>self.assertTrue(pass_test, "gdata is not installed.")</span><br><span style='background:#FFFFF4'>AssertionError: gdata is not installed.</span><br><br><span style='background:#FFFFF4'>======================================================================</span><br><span style='background:#FFFFF4'>FAIL: test_pplacer_supported_version (__main__.QIIMEDependencyFull)</span><br><span style='background:#FFFFF4'>pplacer is in path and version is supported</span><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Traceback (most recent call last):</span><br><span style='background:#FFFFF4'>File "/usr/lib/qiime/bin/print_qiime_config.py", line 655, in test_pplacer_supported_version</span><br><span style='background:#FFFFF4'>"which components of QIIME you plan to use.")</span><br><span style='background:#FFFFF4'>AssertionError: pplacer not found. This may or may not be a problem depending on which components of QIIME you plan to use.</span><br><br><span style='background:#FFFFF4'>======================================================================</span><br><span style='background:#FFFFF4'>FAIL: test_rtax_supported_version (__main__.QIIMEDependencyFull)</span><br><span style='background:#FFFFF4'>rtax is in path and version is supported</span><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Traceback (most recent call last):</span><br><span style='background:#FFFFF4'>File "/usr/lib/qiime/bin/print_qiime_config.py", line 634, in test_rtax_supported_version</span><br><span style='background:#FFFFF4'>"which components of QIIME you plan to use.")</span><br><span style='background:#FFFFF4'>AssertionError: rtax not found. This may or may not be a problem depending on which components of QIIME you plan to use.</span><br><br><span style='background:#FFFFF4'>======================================================================</span><br><span style='background:#FFFFF4'>FAIL: test_sourcetracker_installed (__main__.QIIMEDependencyFull)</span><br><span style='background:#FFFFF4'>sourcetracker is installed</span><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Traceback (most recent call last):</span><br><span style='background:#FFFFF4'>File "/usr/lib/qiime/bin/print_qiime_config.py", line 421, in test_sourcetracker_installed</span><br><span style='background:#FFFFF4'>("SOURCETRACKER_PATH is not set. This is "</span><br><span style='background:#FFFFF4'>AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker.</span><br><br><span style='background:#FFFFF4'>======================================================================</span><br><span style='background:#FFFFF4'>FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)</span><br><span style='background:#FFFFF4'>usearch is in path and version is supported</span><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Traceback (most recent call last):</span><br><span style='background:#FFFFF4'>File "/usr/lib/qiime/bin/print_qiime_config.py", line 714, in test_usearch_supported_version</span><br><span style='background:#FFFFF4'>% ('.'.join(map(str,acceptable_version)), version_string))</span><br><span style='background:#FFFFF4'>AssertionError: Unsupported usearch version. (5, 2, 236).(5, 2, 236) is required, but running<span class=apple-converted-space> </span></span><br><span style='background:#FFFFF4'>USEARCH is not freely redistributable and is thus not included in the</span><br><span style='background:#FFFFF4'>default QIIME package.</span><br><span style='background:#FFFFF4'>You may obtain a personal copy of the 32-bit program at no charge.</span><br><br><span style='background:#FFFFF4'>To use this feature, please go to:</span><br><span style='background:#FFFFF4'><a href="http://www.drive5.com/usearch/download.html">http://www.drive5.com/usearch/download.html</a></span><br><br><span style='background:#FFFFF4'>Download USEARCH v5.2.236, then:</span><br><span style='background:#FFFFF4'>sudo mv usearch* /usr/local/bin/usearch</span><br><span style='background:#FFFFF4'>sudo chmod a+x /usr/local/bin/usearch</span><br><br><span style='background:#FFFFF4'>You probably also want to install USEARCH 6.1 as /usr/local/bin/usearch61</span><br><br><span style='background:#FFFFF4'>.</span><br><br><span style='background:#FFFFF4'>----------------------------------------------------------------------</span><br><span style='background:#FFFFF4'>Ran 35 tests in 0.221s</span><br><br><span style='background:#FFFFF4'>FAILED (failures=6)</span></span><o:p></o:p></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>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?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>Thanks<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:black;background:#FFFFF4'>Alec<o:p></o:p></span></p></div></body></html>