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<TITLE>Re: [phenixbb] AutoBuild help</TITLE>
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<FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Hi Tom,<BR>
<BR>
I’ll give that a try and let you know. Thanks for the fast response.<BR>
<BR>
Tim<BR>
<BR>
<BR>
On 8/18/09 11:40 AM, "Tom Terwilliger" <terwilliger@lanl.gov> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Hi Tim,<BR>
<BR>
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<BR>
<BR>
csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1<BR>
<BR>
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 <a href="http://www.phenix-online.org"><http://www.phenix-online.org></a> . We update PHENIX daily and so your 1.4-3 version is now quite out of date.<BR>
<BR>
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...<BR>
<BR>
All the best,<BR>
Tom T<BR>
<BR>
On Aug 18, 2009, at 9:31 AM, Timothy C. Umland wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
I am new to running the AutoMR and AutoBuild Wizards, and I am having a<BR>
problem getting AutoBuild to run.<BR>
<BR>
I have run AutoMR and it appeared to run fine, yielding a solution. However,<BR>
when it did the default hand-off of the MR solution to AutoBuild, AutoBuild<BR>
crashed. I then tried to run AutoBuild by itself, using the MR solution as<BR>
the input model. Again, AutoBuild crashed.<BR>
<BR>
The error was the same in both cases. I was running AutoMR and AutoBuild<BR>
from the command line. I am running Phenix version 1.4-3 on an Intel Mac (OS<BR>
X 10.5.8).<BR>
<BR>
The AutoBuild error was<BR>
<BR>
<BR>
****************************************************************************<BR>
****<BR>
Failed to carry out AutoBuild_build_cycle:<BR>
<BR>
child process stderr output:<BR>
command: 'csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1'<BR>
sort: invalid option -- 4<BR>
Try `sort --help' for more information.<BR>
****************************************************************************<BR>
****<BR>
<BR>
<BR>
I tried the suggested "sort --help", but at least to me it wasn't helpful. I<BR>
am guessing that I have some incompatibility with my local installation of<BR>
"sort" and Phenix? Any help is appreciated.<BR>
<BR>
<BR>
Thanks,<BR>
<BR>
Tim<BR>
<BR>
<BR>
_______________________________________________<BR>
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</SPAN></FONT></BLOCKQUOTE><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'><BR>
<BR>
<BR>
Thomas C. Terwilliger<BR>
Mail Stop M888<BR>
Los Alamos National Laboratory<BR>
Los Alamos, NM 87545<BR>
<BR>
Tel: 505-667-0072 email: terwilliger@LANL.gov<BR>
Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><BR>
PHENIX web site: <a href="http:www.phenix-online.org">http:www.phenix-online.org</a> <a href="http://www.phenix-online.org"><http://www.phenix-online.org></a> <BR>
ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><BR>
TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a><BR>
CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<HR ALIGN=CENTER SIZE="3" WIDTH="95%"></SPAN></FONT><FONT SIZE="2"><FONT FACE="Monaco, Courier New"><SPAN STYLE='font-size:10.0px'>_______________________________________________<BR>
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</SPAN></FONT></FONT></BLOCKQUOTE><FONT SIZE="2"><FONT FACE="Monaco, Courier New"><SPAN STYLE='font-size:10.0px'><BR>
<BR>
</SPAN></FONT></FONT><FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>-- <BR>
<BR>
Timothy C. Umland, Ph.D.<BR>
<BR>
Hauptman-Woodward Institute� � � �� <BR>
700 Ellicott St.�� �� �� �� �� �� �� �� �� <BR>
Buffalo, NY 14203-1102<BR>
<BR>
Phone: 716-898-8632� �� �� �� �<BR>
Fax:� �716-898-8660� �� �� �� �<BR>
e-mail: umland@hwi.buffalo.edu<BR>
=======================<BR>
<BR>
<BR>
Hauptman-Woodward Medical Research Institute<BR>
and<BR>
Dept. of Structural Biology, University at Buffalo<BR>
<BR>
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