<div dir="ltr">Hi Andrea,<div>I'm sorry for the crash! I'm afraid this looks like a ROSETTA error (as opposed to one in Phenix). These require us asking the Rosetta team to fix them. If you can send all the inputs and the command you used or the .eff file (parameters file from the GUI, using job history/details/) I'll try to run here and get the error and then I'll set up a little command that crashes quickly and I'll contact them to get it fixed.</div><div>All the best,</div><div>Tom T</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 1, 2021 at 1:35 PM Andrea Piserchio <<a href="mailto:andrea.piserchio@gmail.com">andrea.piserchio@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear all,
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">I am trying to run
MR-Rosetta using the gui;</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[ROSETTA_VERSION]:
2021.16+release.8ee4f02</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Phenix version
1.19.2-4158</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">running on Ubuntu
20.04.2 LTS (20.04, focal)</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"> rosetta.run_tests
seems to run without errors.</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">As inputs, I use a
HHpred file, a reflection file, a sequence (FASTA) file and I tried
also providing directly the fragments files from the Robetta server.</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">After generating
some starting models, the runs keep crashing during the rebuild stage
giving the error messages below.</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Is there a way to
troubleshoot this? It does generate some initial models, so it seems
to correctly read the HHPred file and the fasta file.</p><p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br></p><p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Thank you in advance,</p><p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Andrea<br></p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">non-zero return
code: 139</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Failed to run
REBUILD</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">from rebuild.log</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">AN INTERNAL ERROR
HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR
DETAILS.</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Segmentation fault
(core dumped)</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">from
ROSETTA_CRASH.log:</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[END_BACKTRACE]</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[FILE]: SIGSEGV</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[LINE]: 11</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[START_MESSAGE]</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">Segmentation Fault</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent"><br>
</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[END_MESSAGE]</p>
<p style="margin-bottom:0in;line-height:100%;background:none 0% 0% repeat scroll transparent">[END_CRASH_REPORT]</p></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div><div>Tel: 505-431-0010</div><div><br></div></div></div></div></div></div></div></div></div></div>