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. We update PHENIX daily and so your 1.4-3 version is now quite out of date.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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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected]
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