<div dir="ltr"><div><div><div><div><div>Dear Georg,<br><br></div>I did it correctly then for the site.settings file.<br></div>I did install under /home, since I have not root rights. Do you think this might be an issue please?<br><br></div>Many thanks<br></div>Best<br></div>Simone<br><br></div><br><div class="gmail_quote"><div dir="ltr">Il giorno lun 8 ott 2018 alle ore 20:28 Georg Mlynek <<a href="mailto:georg.mlynek@univie.ac.at">georg.mlynek@univie.ac.at</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Dear Simone, <br>
</p>
<p> for site.settings, you should
<br>
overwrite the one in the Rosetta
<br>
directory with the new version, not add
our
<br>
text to the original one.
</p>
Just for curiosity, did you install phenix and rosetta under
usr/local or /home. The first one probably requires running the
installation as root.<br>
<br>
Br, Georg.<br>
<br>
<br>
<div class="m_-2188943791439385733moz-cite-prefix">On 2018-10-08 20:24, Simone Pellegrino
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Billy,</div>
<div><br>
</div>
<div>I have done this. Should I simply replace the previous text
or add to the existing site.settings file please? I did
comment all the previous now.</div>
<div>Best</div>
<div>Simone</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">Il giorno lun 8 ott 2018 alle ore 17:38 Billy
Poon <<a href="mailto:BKPoon@lbl.gov" target="_blank">BKPoon@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">
<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" target="_blank">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="m_-2188943791439385733m_8660578833603473405gmail_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" 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>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_-2188943791439385733m_8660578833603473405m_-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 : <a class="m_-2188943791439385733moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov" target="_blank">NWMoriarty@LBL.gov</a><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_-2188943791439385733m_8660578833603473405m_-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>
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-- <br>
<div dir="ltr" class="m_-2188943791439385733m_8660578833603473405m_-3232744231623291837gmail_signature" data-smartmail="gmail_signature">Dr. Simone Pellegrino<br>
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67404 Illkirch Cedex<br>
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<div dir="ltr" class="m_-2188943791439385733gmail_signature" data-smartmail="gmail_signature">Dr. Simone Pellegrino<br>
I.G.B.M.C.<br>
1, Rue Laurent Fries<br>
67404 Illkirch Cedex<br>
France</div>
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