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
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 We update PHENIX daily and so your 1.4-3 version is now quite out of date.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
_______________________________________________ phenixbb mailing list [email protected] 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: [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
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"
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 [email protected] 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: [email protected] 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 [email protected] 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: [email protected] ======================= Hauptman-Woodward Medical Research Institute and Dept. of Structural Biology, University at Buffalo
participants (2)
-
Timothy C. Umland -
Tom Terwilliger