[phenixbb] AutoBuild help

Tom Terwilliger terwilliger at lanl.gov
Tue Aug 18 08:40:54 PDT 2009

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  

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.  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PHENIX daily and so your 1.4-3 version is now quite out of date.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
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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