Rosetta’s building is OK, but the program is running failed

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

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…

[Anonymous]

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?

[Anonymous]

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 ‘{}’ ;

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