[phenixbb] Rosetta installation

Nigel Moriarty nwmoriarty at lbl.gov
Sun Oct 8 08:30:40 PDT 2017


Can you send me the directory that was created by rosetta.run_tests.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Sat, Oct 7, 2017 at 9:52 AM, Daniele de Sanctis <de.sanctisd at gmail.com>
wrote:

> Hi all
>
> I have some trouble installing rosetta. I followed the instruction as in
> https://www.phenix-online.org/documentation/reference/rosetta_install.html
>
> and everything went ok up to
>
> % rosetta.build_phenix_interface nproc=n
>
> but then
>
> % rosetta.run_tests
>
> fails with
>
> Rosetta command-line arguments:
>   -parser:protocol /buffer/desancti/xtal/rosetta_
> src_2016.32.58837_bundle/main/source/src/apps/public/
> crystal_refinement/low_resolution_refine.xml
>   -s 1yjp_rosetta_in.pdb
>   -mtzfile 1yjp_rosetta_data.mtz
>   -run:preserve_header
>   -crystal_refine
>   -parser:script_vars symmdef=1yjp_rosetta.symm
>   -parser:script_vars bfactstrat=individual
>   -parser:script_vars map_type=Auto
>   -score:weights talaris2013_cart
>   -nstruct 1
>
> Generating 2 models on 1 processors...
>
> DEBUG dumping error message
> ERROR: Rosetta exited with status 139
> stderr output:
> Segmentation fault (core dumped)
> Traceback (most recent call last):
>   File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../
> modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in
> <module>
>     run(sys.argv[1:], create_dir=True)
>   File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../
> modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run
>     debug=params.output.debug)
>   File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/
> phenix/phenix/rosetta/refine.py", line 313, in __init__
>     self.run_jobs()
>   File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/
> phenix/phenix/rosetta/refine.py", line 388, in run_jobs
>     check_result(result)
>   File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/
> phenix/phenix/rosetta/refine.py", line 379, in check_result
>     raise RuntimeError("Aborted due to error in job %d." % result.job_id)
> RuntimeError: Aborted due to error in job 1.
>
>
> Any idea?
>
> thanks
>
> Daniele
>
>
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