<div dir="ltr"><div dir="ltr">Hi Simone,<div><br></div><div>With later compilers (GCC >= 5.1), you need to add the site.settings file from <a href="https://www.phenix-online.org/documentation/extras/site.settings">https://www.phenix-online.org/documentation/extras/site.settings</a>. That adds a flag that correctly links Phenix and Rosetta.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Oct 8, 2018 at 3:15 AM Simone Pellegrino <<a href="mailto:simonpelle81@gmail.com">simonpelle81@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi Andy and Nigel,</div><div><br></div><div>I started from scratch again and did the following.</div><div><br></div><div>1) I installed latest CentOS6 phenix and installed onto an Ubuntu 18.04 system.</div><div>2) I downloaded Rosetta 2018.31 and compiled by running the scons.py code.</div><div>3) Then I followed the instructions form Nigel and compiled the interface between phenix and Rosetta by doing all the steps as written in the installation procedure.</div><div>4) Still having the same issue. <br></div><div><br></div><div>Any clue about what am I doing wrong please?</div><div>Many thanks</div><div>Best</div><div>Simone</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">Il giorno sab 6 ott 2018 alle ore 19:59 Andy Watkins <<a href="mailto:andy.watkins2@gmail.com" target="_blank">andy.watkins2@gmail.com</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">That seems like an issue unrelated to rosetta_refine per se but instead related to your Rosetta configuration in general. I don't know much about rosetta_refine, but does it use any scripts from the Rosetta tools repository, or could you be invoking a test that uses some of those scripts?<div><br></div><div>parse_tag is a Python component that's invoked by some of the python scripts in ERRASER, for example, and if it can't find it then it means that Rosetta/tools/rna_tools/bin isn't on your $PYTHONPATH.</div></div><br><div class="gmail_quote"><div dir="ltr">On Sat, Oct 6, 2018 at 11:50 AM Simone Pellegrino <<a href="mailto:simonpelle81@gmail.com" target="_blank">simonpelle81@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div>Hi Nigel,</div><div><br></div><div>to install Phenix I followed the recommended procedure as specified in the online manual. <br></div><div>Then to install Rosetta I finally followed one of the response on the Rosetta forum (can't remember now the exact thread)<br></div><div> and I came to this last error of the <br></div><div><br></div><div>ImportError: No module named parse_tag</div><div><br></div><div>Many thnaks for your help.</div><div>Best</div><div>Simone</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr">Il giorno sab 6 ott 2018 alle ore 17:41 Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">This looks very strange. The error is in the file in the installer directories. This should not be the case. Can you provide more details on what you did to install Phenix etc.<div><br clear="all"><div><div dir="ltr" class="m_-3232744231623291837m_-5507462056908581581m_-481465661778165379m_-2321073063152197816gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Sat, Oct 6, 2018 at 4:15 AM Simone Pellegrino <<a href="mailto:simonpelle81@gmail.com" target="_blank">simonpelle81@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Dear all,</div><div><br></div><div>I encounter a problem running the rosetta.run_tests after having compiled rosetta for interfacing with phenix. I have the following error:</div><div><br></div><div><br></div><div>DEBUG dumping error message<br>ERROR: Rosetta exited with status 139<br>stderr output:<br>Segmentation fault (core dumped)<br>Traceback (most recent call last):<br> File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module><br> run(sys.argv[1:], create_dir=True)<br> File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run<br> debug=params.output.debug)<br> File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__<br> self.run_jobs()<br> File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 387, in run_jobs<br> check_result(result)<br> File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 378, in check_result<br> raise RuntimeError("Aborted due to error in job %d." % result.job_id)<br>RuntimeError: Aborted due to error in job 1.<br><br></div><div>Could you please help me in solving this issue?</div><div>Many thanks in advance</div><div>Best regards</div><div>Simone<br></div><div><br>-- <br><div dir="ltr" class="m_-3232744231623291837m_-5507462056908581581m_-481465661778165379m_-2321073063152197816m_3511104543618599767gmail_signature">Dr. Simone Pellegrino<br>I.G.B.M.C.<br>1, Rue Laurent Fries<br>67404 Illkirch Cedex<br>France</div></div></div></div></div>
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