[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 update PHENIX daily and so your 1.4-3 version is now quite out of date.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
>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> 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
> 
> 
> 
>  
> 
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb


-- 

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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