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 We update PHENIX daily and so your 1.4-3 version is now quite out of date.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