[phenixbb] AutoBuild help
Timothy C. Umland
umland at hwi.buffalo.edu
Tue Aug 18 08:49:48 PDT 2009
Hi Tom,
I¹ll give that a try and let you know. Thanks for the fast response.
Tim
On 8/18/09 11:40 AM, "Tom Terwilliger" <terwilliger at lanl.gov> wrote:
> Hi Tim,
>
> I am sorry for the trouble! I have not seen this particular error before, but
> it is coming from AutoBuild running a sub-process with the command
>
> csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1
>
> Can you possibly update to a recent "nightly build" version of PHENIX, as this
> may have fixed the problem? You can get a nightly build from the download
> page of PHENIX at www.phenix-online.org <http://www.phenix-online.org> . We
> update PHENIX daily and so your 1.4-3 version is now quite out of date.
>
> If that does not do it, can you send me the contents of the file listed above?
> I am puzzled by the word "sort" as there shouldn't be any sorting there at
> all...
>
> All the best,
> Tom T
>
> On Aug 18, 2009, at 9:31 AM, Timothy C. Umland wrote:
>
>>
>> I am new to running the AutoMR and AutoBuild Wizards, and I am having a
>> problem getting AutoBuild to run.
>>
>> I have run AutoMR and it appeared to run fine, yielding a solution. However,
>> when it did the default hand-off of the MR solution to AutoBuild, AutoBuild
>> crashed. I then tried to run AutoBuild by itself, using the MR solution as
>> the input model. Again, AutoBuild crashed.
>>
>> The error was the same in both cases. I was running AutoMR and AutoBuild
>> from the command line. I am running Phenix version 1.4-3 on an Intel Mac (OS
>> X 10.5.8).
>>
>> The AutoBuild error was
>>
>>
>> ****************************************************************************
>> ****
>> Failed to carry out AutoBuild_build_cycle:
>>
>> child process stderr output:
>> command: 'csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1'
>> sort: invalid option -- 4
>> Try `sort --help' for more information.
>> ****************************************************************************
>> ****
>>
>>
>> I tried the suggested "sort --help", but at least to me it wasn't helpful. I
>> am guessing that I have some incompatibility with my local installation of
>> "sort" and Phenix? Any help is appreciated.
>>
>>
>> Thanks,
>>
>> Tim
>>
>>
>> _______________________________________________
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>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel: 505-667-0072 email: terwilliger at LANL.gov
> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org <http://www.phenix-online.org>
> ISFI Integrated Center for Structure and Function Innovation web site:
> http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
>
>
>
>
>
>
>
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> phenixbb at phenix-online.org
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--
Timothy C. Umland, Ph.D.
Hauptman-Woodward Institute
700 Ellicott St.
Buffalo, NY 14203-1102
Phone: 716-898-8632
Fax: 716-898-8660
e-mail: umland at hwi.buffalo.edu
=======================
Hauptman-Woodward Medical Research Institute
and
Dept. of Structural Biology, University at Buffalo
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