[phenixbb] Rosetta installation problems

[Simone Pellegrino]

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 <
andy.watkins2 at gmail.com> ha scritto:

> 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 <simonpelle81 at gmail.com>
> wrote:
>
>> 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 <
>> nwmoriarty at lbl.gov> ha scritto:
>>
>>> 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 : NWMoriarty at LBL.gov
>>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>>>
>>>
>>> On Sat, Oct 6, 2018 at 4:15 AM Simone Pellegrino <simonpelle81 at gmail.com>
>>> wrote:
>>>
>>>> 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
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>
>>>
>>
>> --
>> Dr. Simone Pellegrino
>> I.G.B.M.C.
>> 1, Rue Laurent Fries
>> 67404 Illkirch Cedex
>> France
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>

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