# Rosetta's building is OK, but the program is running failed

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Rosetta's building is OK, but the program is running failed
#1

Hi,
I encountered a problem with rosetta that I can not solve it myself. could anyone do me a favor.
I installed rosetta on Cent Os, and everything looks OK. But when I ran the test command "phenix_regression.wizards.test_command_line_rosetta_quick_tests", it failed as following:

Running all command_line tests
Number of tests to run: 38
=================================================================
Running test_autobuild
OK
=================================================================
Running test_autobuild_double
OK
=================================================================
Running test_average
OK
=================================================================
Running test_average_double
OK
=================================================================
Running test_denmod_refine_after_mr
OK
=================================================================
Running test_denmod_refine_after_mr_double
OK
=================================================================
Running test_hhr
OK
=================================================================
Running test_mr_rescoring
OK
=================================================================
Running test_mr_rescoring_double
OK
=================================================================
Running test_place_model
OK
=================================================================
Running test_place_model_double
OK
=================================================================
Running test_prerefine
OK
=================================================================
Running test_prerefine_double
FAILED TO RUN: test_prerefine_double
*****************************************************
Error: test_command_line_rosetta_quick_tests failed.

It failed at the rosetta prerefine step. I tried to run the shell script "test_prerefine_double.com" in the "test_prerefine_double" direcory, it shows up the following:
==============================================================================
Starting sub-processes Group of rosetta rebuild...
==============================================================================

Splitting work into 1 jobs and running with 1 processors using sh
background=None in /xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2

Starting job 1...Log will be: /xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.log
Sorry: mr_rosetta failed...
child process stderr output:
command: 'sh /xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1'
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/rave:/xtal_programs/USF/sbin:/xtal_programs/USF/spasm:/xtal_programs/USF/voidoo:/xtal_programs/USF/xutil:/xtal_programs/O:/xtal_programs/O/data/omac:/xtal_programs/clustalw-2.1:/xtal_programs/multalin:/xtal_programs/ESPript-2_3-www-3_05/bin:/xtal_programs/shelx/linux:/xtal_programs/graphviz-2.20.2/bin:/xtal_programs/fasta-35.4.1/bin:/xtal_programs/molscript-2.1.2:/xtal_programs/bobscript/bin:/xtal_programs/XDS:/xtal_programs/HKL2000:/xtal_programs/pseudo/bin:/xtal_programs/OASIS-2004/bin:/xtal_programs/sapipro:/xtal_programs/ha_ncs:/xtal_programs/snb2.2p1/bin:/xtal_programs/dssp:/xtal_programs/hole2/exe:/xtal_programs/automar:/xtal_programs/whatcheck:/xtal_programs/yasara:/xtal_programs/MoProSuite/bin-Linux:/xtal_programs/MoProSuite:/xtal_programs/vmd-1.9beta2:/xtal_programs/3D_Dock/progs:/xtal_programs/3D_Dock/multidock:/xtal_programs/REPLACE/bin/Linux:/xtal_programs/MIFit:/xtal_programs/Raster3D_2.7s:/xtal_programs/chimera/bin:/xtal_programs/untangle-0.7:/xtal_programs/xdsme-0.4.9/bin/noarch:/xtal_programs/pymol/apbs-1.0.0/bin:/xtal_programs/pymol/apbs-1.0.0/share/tools/manip:/xtal_programs/solve-2.13/bin:/xtal_programs/USF/dejavu:: No such file or directory
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/rave:: No such file or directory
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/sbin:: No such file or directory
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/spasm:: No such file or directory
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/voidoo:: No such file or directory
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/USF/xutil:/xtal_programs/O:: No such file or directory
/xtal_programs/rosetta3.2.1/test_prerefine_double/GROUP_OF_ROSETTA_REBUILD_2/RUN_FILE_1.sh: line 4: :/xtal_programs/O/data/omac:/xtal_programs/clustalw-2.1:/xtal_programs/multalin:/xtal_programs/ESPript-2_3-www-3_05/bin:/xtal_programs/shelx/linux:/xtal_programs/graphviz-2.20.2/bin:/xtal_programs/fasta-35.4.1/bin:/xtal_programs/molscript-2.1.2:/xtal_programs/bobscript/bin:/xtal_programs/XDS:/xtal_programs/HKL2000:/xtal_programs/pseudo/bin:/xtal_programs/OASIS-2004/bin:/xtal_programs/sapipro:/xtal_programs/ha_ncs:/xtal_programs/snb2.2p1/bin:/xtal_programs/dssp:/xtal_programs/hole2/exe:/xtal_programs/automar:/xtal_programs/whatcheck:/xtal_programs/yasara:/xtal_programs/MoProSuite/bin-Linux:/xtal_programs/MoProSuite:/xtal_programs/vmd-1.9beta2:/xtal_programs/3D_Dock/progs:/xtal_programs/3D_Dock/multidock:/xtal_programs/REPLACE/bin/Linux:/xtal_programs/MIFit:/xtal_programs/Raster3D_2.7s:/xtal_programs/chimera/bin:/xtal_programs/untangle-0.7:/xtal_programs/xdsme-0.4.9/bin/noarch: No such file or directory.

I can not configure where is the problem, I have sat the path in a .cshrc file. It seems the program can not find out where's rosetta?

I also have tested on a phenix.mr_rosetta case, it also failed at the prerefine stage. The phenix commands such as molecular replacement, density average, autobuild and refinement works, but can not go on with rosetta.

Post Situation:
Fri, 2012-02-24 04:51
yancy

I don't recognize a single line of any of that as being from Rosetta - those all look like phenix (or even shell) outputs. You should try to find a phenix person to ask.

Where is Rosetta installed? The only rosetta-seeming path there is "xtal_programs/rosetta3.2.1/test_prerefine_double". I know no directory "test_prerefine_double" ships with 3.2.1, so I don't know if you made it or if Phenix creates it or what.

Is it supposed to be looking through those huge colon-agglomerated paths or should Rosetta be specified as a single path?

Did you compile Rosetta...? It comes as source code not binaries.

Fri, 2012-02-24 06:33
smlewis

I compiled Rosetta in the path /xtal_programs/rosetta3.2.1, and it took one hour and ended with "scons: done building targets." and I also set the Path in the .cshrc file, I wrote "setenv PHENIX_ROSETTA_PATH /xtal_programs/rosetta3.2.1" there.

"test_prerefine_double" is one of the directory created by the phenix rosetta test command "phenix_regression.wizards.test_command_line_rosetta_quick_testsls".
It failed at the prerefine step.

when I ran a script for example "Standard run of mr_rosetta", it failed when it needed to rebuild the model with rosetta.
it seems phenix can not find the right path of rosetta? Should I write something in the phenix scripts so that it can know where is rosetta?

Fri, 2012-02-24 17:47
yancy

If Rosetta compiled, it's a Phenix thing, not a Rosetta thing. I've never installed phenix (nor have the usual support people here). Here's what their FAQ says:

http://www.phenix-online.org/documentation/faqs.htm#anch84

Problems installing Rosetta? Here are some suggestions:

Download rosetta_source and rosetta_database separately. The bundle doesn't contain all the files.
Compilation fails on RHEL 6.1 (gcc 4.5 issue) but sails on RHEL 5.5.
$PHENIX_ROSETTA_PATH must point to the Rosetta installation directory (where rosetta_source and rosetta_database sit). (Note there was a typo in documentation with ROSETTTA instead of ROSETTA; fixed now.) all directories in the Rosetta installation must be made accessible to users: find$PHENIX_ROSETTA_PATH -type d -exec chmod 755 '{}' \;

Sun, 2012-02-26 10:36
smlewis

user@user-HCL-Desktop:~/csrosetta3$./install.py delete pyc files from AUTO-DETECTED: Running on linux... please any any one can help me out this problem...... AUTO-DETECTION: check$PATH
AUTO-DETECTION: look in $HOME/rosetta AUTO-DETECTION FAILED: cannot find ROSETTA binaries. Run with -rosetta to point to binaries if toolbox is intended for automatic setup of CS-ROSETTA calculations AUTO-DETECTION FAILED: cannot find ROSETTA database. Run with -rosetta_database to point to database if toolbox is intended for automatic setup of CS-ROSETTA calculations check whether dunbrack library can be loaded from the binary file... /bin/sh: 1: None/score_jd2.default.linuxgccrelease: not found /bin/sh: 1: None/score_jd2.default.linuxgccrelease: not found Traceback (most recent call last): File "./install.py", line 330, in if not check_dunbrack_library( rosetta_db_path, rosetta_bin, build, platform, final_msgs ): File "./install.py", line 322, in check_dunbrack_library os.remove('score.sc') OSError: [Errno 2] No such file or directory: 'score.sc' user@user-HCL-Desktop:~/csrosetta3$

Thank you...

Sat, 2014-01-04 06:12
krishnakant