[phenixbb] MR-Rosetta crashes during rebuild

[Tom Terwilliger]

Hi Andrea,
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.
All the best,
Tom T

On Thu, Jul 1, 2021 at 1:35 PM Andrea Piserchio <andrea.piserchio at gmail.com>
wrote:

> Dear all,
>
> I am trying to run MR-Rosetta using the gui;
>
> [ROSETTA_VERSION]: 2021.16+release.8ee4f02
>
> Phenix version 1.19.2-4158
>
> running on Ubuntu 20.04.2 LTS (20.04, focal)
>
>
> rosetta.run_tests seems to run without errors.
>
>
> 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.
>
>
> After generating some starting models, the runs keep crashing during the
> rebuild stage giving the error messages below.
>
>
> 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.
>
>
> Thank you in advance,
>
> Andrea
>
>
>
> non-zero return code: 139
>
> Failed to run REBUILD
>
>
> from rebuild.log
>
> AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF
> ROSETTA_CRASH.log FOR DETAILS.
>
> Segmentation fault (core dumped)
>
>
> from ROSETTA_CRASH.log:
>
>
> [END_BACKTRACE]
>
>
> [FILE]: SIGSEGV
>
> [LINE]: 11
>
> [START_MESSAGE]
>
> Segmentation Fault
>
>
> [END_MESSAGE]
>
> [END_CRASH_REPORT]
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-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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