Re: [phenixbb] Rosetta installation problems

Hi Billy, 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. Best Simone Il giorno lun 8 ott 2018 alle ore 17:38 Billy Poon ha scritto:

Hi Simone,

With later compilers (GCC >= 5.1), you need to add the site.settings file from https://www.phenix-online.org/documentation/extras/site.settings. That adds a flag that correctly links Phenix and Rosetta.

-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

On Mon, Oct 8, 2018 at 3:15 AM Simone Pellegrino wrote:

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Hi Andy and Nigel,

I started from scratch again and did the following.

1) I installed latest CentOS6 phenix and installed onto an Ubuntu 18.04 system. 2) I downloaded Rosetta 2018.31 and compiled by running the scons.py code. 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. 4) Still having the same issue.

Any clue about what am I doing wrong please? Many thanks Best Simone

Il giorno sab 6 ott 2018 alle ore 19:59 Andy Watkins < [email protected]> ha scritto:

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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?

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.

On Sat, Oct 6, 2018 at 11:50 AM Simone Pellegrino < [email protected]> wrote:

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Hi Nigel,

to install Phenix I followed the recommended procedure as specified in the online manual. Then to install Rosetta I finally followed one of the response on the Rosetta forum (can't remember now the exact thread) and I came to this last error of the

ImportError: No module named parse_tag

Many thnaks for your help. Best Simone

Il giorno sab 6 ott 2018 alle ore 17:41 Nigel Moriarty < [email protected]> ha scritto:

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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.

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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Sat, Oct 6, 2018 at 4:15 AM Simone Pellegrino < [email protected]> wrote:

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Dear all,

I encounter a problem running the rosetta.run_tests after having compiled rosetta for interfacing with phenix. I have the following error:

DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): 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> run(sys.argv[1:], create_dir=True) 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 debug=params.output.debug) 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__ self.run_jobs() 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 check_result(result) 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 raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1.

Could you please help me in solving this issue? Many thanks in advance Best regards Simone

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France