<p dir="ltr">Dear Tony Travis, </p>
<p dir="ltr">Thank you very much. I will try doing that once I get back to my computer. Thank you again very much. </p>
<p dir="ltr">Sincerely, </p>
<p dir="ltr">David Bradshaw</p>
<div class="gmail_extra"><br><div class="gmail_quote">On Aug 13, 2016 12:20 PM, "Tony Travis" <<a href="mailto:tony.travis@minke-informatics.co.uk">tony.travis@minke-informatics.co.uk</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 12/08/16 21:00, David Bradshaw wrote:<br>
> Dear Whom It May Concern,<br>
><br>
> I may have accidentally sent this email to the wrong place initially, I<br>
> apologize. I upgraded to Ubuntu 16.04 and now there are items within<br>
> qiime that are not working. I imagine I may have removed some essential<br>
> items during the upgrade? What would be the best way to fix this? Below<br>
> are some of the errors I am encountering with the print_qiime_config_all<br>
> and join_paired_ends commands.<br>
<br>
Hi, David.<br>
<br>
I've also upgraded Bio-Linux 8 on my laptop "beluga" to Ubuntu 16.04 LTS<br>
and there are a few problems: I've confirmed your bug report, which is<br>
caused by the "xenial" (16.04) version of python-skbio taking<br>
prece4dence over Tim's Bio-Linux version:<br>
<br>
> root@beluga:~# apt-cache policy python-skbio<br>
> python-skbio-doc:<br>
> Installed: (none)<br>
> Candidate: 0.4.1-1<br>
> Version table:<br>
> 0.4.1-1 500<br>
> 500 <a href="http://gb.archive.ubuntu.com/ubuntu" rel="noreferrer" target="_blank">http://gb.archive.ubuntu.com/<wbr>ubuntu</a> xenial/universe amd64 Packages<br>
> 500 <a href="http://gb.archive.ubuntu.com/ubuntu" rel="noreferrer" target="_blank">http://gb.archive.ubuntu.com/<wbr>ubuntu</a> xenial/universe i386 Packages<br>
> python-skbio:<br>
> Installed: 0.4.1-1<br>
> Candidate: 0.4.1-1<br>
> Version table:<br>
> *** 0.4.1-1 500<br>
> 500 <a href="http://gb.archive.ubuntu.com/ubuntu" rel="noreferrer" target="_blank">http://gb.archive.ubuntu.com/<wbr>ubuntu</a> xenial/universe amd64 Packages<br>
> 100 /var/lib/dpkg/status<br>
> 0.2.3-0biolinux2 500<br>
> 500 <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu" rel="noreferrer" target="_blank">http://ppa.launchpad.net/nebc/<wbr>bio-linux/ubuntu</a> trusty/main amd64 Packages<br>
<br>
Force the version to make "apt" downgrade to the Bio-Linux 8 version:<br>
<br>
> root@beluga:~# apt install python-skbio=0.2.3-0biolinux2<br>
> Reading package lists... Done<br>
> Building dependency tree<br>
> Reading state information... Done<br>
> The following packages were automatically installed and are no longer required:<br>
> python-bz2file python-cachecontrol python-contextlib2 python-requests<br>
> Use 'sudo apt autoremove' to remove them.<br>
> The following packages will be DOWNGRADED:<br>
> python-skbio<br>
> 0 to upgrade, 0 to newly install, 1 to downgrade, 0 to remove and 0 not to upgrade.<br>
> Need to get 257 kB of archives.<br>
> After this operation, 1,953 kB disk space will be freed.<br>
> Do you want to continue? [Y/n]<br>
> Get:1 <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu" rel="noreferrer" target="_blank">http://ppa.launchpad.net/nebc/<wbr>bio-linux/ubuntu</a> trusty/main amd64 python-skbio amd64 0.2.3-0biolinux2 [257 kB]<br>
> Fetched 257 kB in 0s (715 kB/s)<br>
> dpkg: warning: downgrading python-skbio from 0.4.1-1 to 0.2.3-0biolinux2<br>
> (Reading database ... 522743 files and directories currently installed.)<br>
> Preparing to unpack .../python-skbio_0.2.3-<wbr>0biolinux2_amd64.deb ...<br>
> Unpacking python-skbio (0.2.3-0biolinux2) over (0.4.1-1) ...<br>
> Setting up python-skbio (0.2.3-0biolinux2) ...<br>
> root@beluga:~# apt-cache policy python-skbio<br>
> python-skbio:<br>
> Installed: 0.2.3-0biolinux2<br>
> Candidate: 0.4.1-1<br>
> Version table:<br>
> 0.4.1-1 500<br>
> 500 <a href="http://gb.archive.ubuntu.com/ubuntu" rel="noreferrer" target="_blank">http://gb.archive.ubuntu.com/<wbr>ubuntu</a> xenial/universe amd64 Packages<br>
> *** 0.2.3-0biolinux2 500<br>
> 500 <a href="http://ppa.launchpad.net/nebc/bio-linux/ubuntu" rel="noreferrer" target="_blank">http://ppa.launchpad.net/nebc/<wbr>bio-linux/ubuntu</a> trusty/main amd64 Packages<br>
> 100 /var/lib/dpkg/status<br>
><br>
<br>
There are still many problems with the OpenMPI support for QIIME, but at<br>
least this is a step in the right direction :-)<br>
<br>
HTH,<br>
<br>
Tony.<br>
<br>
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</blockquote></div></div>