Hi Jermaine, Thank you! That helps eliminate a lot of possible reasons for the problem. Now your mr_rosetta log file should look something like the one below near the end, as you mention that it got as far as rescoring. My next quesetion is...is the part "Collecting all runs now" there? Also what is in the file .../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/JOBS_RUNNING (Does it indicate all jobs finished)? It's fine to continue this off-list until we figure out the answer if you like. All the best, Tom Starting sub-processes Group of rescore MR rosetta:Rescoring set of rosetta models...============================================================================== Splitting work into 4 jobs and running with 20 processors using qsubbackground=False in /net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_r osetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1 Starting job 1...Log will be: /net/omega/raid1/scratch1/terwill/blind_tests/all_ cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.logStarting job 2...Log will be: /net/omega/raid1/scratch1/terwill/blind_tests/all_ cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log Collecting all runs now Collecting run_file: /net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_ rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1info_file: /net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_rosetta_fr om_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/INFO_FILE_1 method: mr_rosettalogfile: /net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log Reading pickle file from /net/omega/raid1/scratch1/terwill/blind_tests/all_cases/mr_rosetta_from_templates/3_cab55348/MR_ROSETTA_7/GROUP_OF_RESCORE_MR_ROSETTA_1 /RUN_1/results.pkl

...

I ran the tests as requested and got an "ALL COMMAND_LINE TESTS OK" so things appear to be working fine. I am submitting my job to a cluster using a script that qsubs nodes=1:ppn=4,walltime=160:00:00. Then executes another script that sources phenix, sets an export phenix_rosetta path an runs "phenix.mr_rosetta mr_rosetta_params.eff ".

JJ

On Tue, May 10, 2011 at 9:56 PM, Thomas C. Terwilliger

...

wrote:

...

Hi Jermaine, I am sorry for the trouble! I am wondering if rosetta is working quite right? Can you possibly run the regression tests on mr_rosetta:

phenix_regression.wizards.test_command_line_rosetta_quick_tests

and see if that helps diagnose the problem? All the best, Tom T

...

...

I have been trying a standard run of mr_rosetta and I have stopped at the same point (output below). 32 folders were created in the GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all say that saved overall results to a .../results.pkl and the Run log file states that each job finished. But no further files were written in the Work folder under each RUN folder and I am assuming there should be a folder with my final 20 Rosetta models somewhere. Does this mean there was a failure in a subscript?

==============================================================================

...

Starting sub-processes Group of rescore MR rosetta:Rescoring set of rosetta models...

==============================================================================

...

Splitting work into 32 jobs and running with 4 processors using sh background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1

Starting job 1...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log Starting job 2...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log

thanks, JJ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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