[phenixbb] mr_rosetta problems

Ian Slaymaker iamslaymaker at gmail.com
Tue Aug 7 10:32:05 PDT 2012 

I ran the suggested test, and checked my fragment files. The fragment files
seem to be spic and span, but the test still errored out with this and the
rebuild.log file looked the same.
My fragment files look like this :

position:            1 neighbors:          200

 1je5 A   137 M L  -94.840  117.510 -178.319    2.237   10.852    31.857 3
    0.000 P  1 F  1
 1je5 A   138 E L  -71.213  -39.327  177.116    2.237   10.852    31.857 3
    0.000 P  1 F  1
 1je5 A   139 D L -112.228   93.181 -175.069    2.237   10.852    31.857 3
    0.000 P  1 F  1
 1je5 A   140 V L  -70.333  120.424  178.205    2.237   10.852    31.857 3
    0.000 P  1 F  1

Starting mr_rosetta_rebuild
Date: Tue Aug  7 10:15:26 2012
Directory: /test_prerefine

HOST = hpc-cmb
HOSTTYPE = x86_64-linux
USER = slaymake
PID = 30481
Checking rosetta paths:
  rosetta binary:
/home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_source/bin/mr_protocols.default.
                                                  linuxgccrelease
  database_dir: /home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_database
  script_dir:
/home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_source/src/apps/public/electron_dens
                                                  ity
pilot_script_dir:
/home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_source/src/apps/pilot/frank/

Sequence rewritten to /test_prerefine/WORK_2/EDITED_seq.dat
                                   :
 > sequence information
AQLMDMRD

Changing to work directory: /test_prerefine/WORK_2


Rebuilding the model/test_prerefine/coords1.pdb
with rosetta
Running mr_rosetta_rebuild without map information

Generating 1 rebuilt models
================================================================================
Reading model from/test_prerefine/coords1.pdb
================================================================================
ALIGNMENT LINES:
## TARGET coord
# hhsearch
scores_from_program: 0 1.00
0 AQLMDMRD
0 -QLMDMRD
--

Alignment file matches PDB file
Start position of target sequence in sequence file:  0

Aligned model for comparison:
/test_prerefine/WORK_2/WORK_1/aligned_model.pdb
Log for rebuilding: /test_prerefine/WORK_2/WORK_1/rebuild.log

******************* ERROR ENDING ***************
Failed to run REBUILD...see log file in
/test_prerefine/WORK_2/WORK_1/rebuild.log

******************* ERROR ENDING ***************
hpc-cmb(231):


On Tue, Aug 7, 2012 at 10:05 AM, Andreas Förster <docandreas at gmail.com>wrote:

> Hi Ian,
>
> I had a similar issue once.  Check that your fragment files start with a
> line reading
>
>  position:            1 neighbors:          200
>
> or something like this.  If there's html code (download artifact), remove
> it.  Same at the end of the files.  Last line should be blank and before
> that, only fragments.
>
>
>
> Andreas
>
>
>
>
> On 07/08/2012 5:52, Terwilliger, Thomas C wrote:
>
>> Hi Ian,
>>
>> I think this part of the error message is the best hint:
>>
>> finished reading top 0 0mer fragments from
>> file/dataFiles/aat000_03_05.**200_v1_3
>>
>> I am guessing there is something odd about the fragment file all right.
>> You could try supplying this file in one of the tests and see if it
>> causes the test to fail:
>>
>> phenix_regression.wizards.**test_command_line_rosetta_**quick
>> test_prerefine
>>
>> then:...
>>
>> cd test_prerefine
>> phenix.mr_rosetta seq_file=seq.dat search_models=coords1.pdb
>> start=place_model stop=place_model data=fobs.mtz is_sub_process=True
>> already_placed=true refine_after_mr=False run_prerefine=True
>> number_of_prerefine_models=1 rosetta_fixed_seed=1571
>> fragment_files=/Users/terwill/**unix/PHENIX/phenix-dev-894/**
>> phenix/phenix/rosetta/dummy_**fragments_file_3.gz
>> fragment_files=/Users/terwill/**unix/PHENIX/phenix-dev-894/**
>> phenix/phenix/rosetta/dummy_**fragments_file_9.gz
>>
>> Then, try above with your fragment files...
>>
>> That might point out the problem!
>> All the best,
>> Tom T
>>
>>
>>
>>
>>
>>
>> *From:* phenixbb-bounces at phenix-**online.org<phenixbb-bounces at phenix-online.org>
>>
>> [phenixbb-bounces at phenix-**online.org<phenixbb-bounces at phenix-online.org>]
>> on behalf of Ian Slaymaker
>> [slaymake at usc.edu]
>> *Sent:* Tuesday, August 07, 2012 10:21 AM
>> *To:* phenixbb at phenix-online.org
>> *Subject:* [phenixbb] mr_rosetta problems
>>
>>
>> I am trying to get mr_rosetta working on our cluster and am running into
>> some problems I am not sure how to solve. The
>> phenix_regression.wizards.**test_command_line_rosetta_**quick_tests tests
>> went smoothly were completed.
>>
>> However, my first test run with all the defaults (not submitted to
>> multiple processors) using my reflection file, HHR analysis file,
>> sequence file, and the 2 fragment files failed with the below errors. I
>> checked all the files, and it seems this is a problem with the fragment
>> files but I am not sure exactly what they are supposed to look like.
>>
>> I thought it could be because our cluster doesnt have access to any
>> outside networks...is this a problem with rosetta not being able to
>> download pdb files? if so, is there a way to supply them internally?
>> The aligned model looks somewhat what I expected it to (same beta sheet
>> arrangement) but it seems to be incomplete.
>> Any help would be very much appreciated!
>>
>>
>>
>> Splitting work into 100 jobs and running with 1 processors using sh
>> background=None in /MR_ROSETTA_1/GROUP_OF_**ROSETTA_REBUILD_1/RUN_1/**
>> REBUILD_IN_SETS_1
>>
>> Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_**
>> ROSETTA_REBUILD_1/RUN_1/**REBUILD_IN_SETS_1/RUN_FILE_1.**log
>>
>> ******************* ERROR ENDING ***************
>> mr_rosetta failed...
>>
>> ****************************************************************
>> ********************
>> Sorry, a subprocess has failed...
>>
>> END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_**ROSETTA_REBUILD_1/RUN_1/**
>> REBUILD_IN_SETS_1/RUN_FILE_1.**log :
>>
>> to match the actual PDB sequence:
>> (protein sequence)
>> New alignment line 4 for PDB:
>> (protein sequence)
>>
>>
>> Start position of target sequence in sequence file:  0
>>
>> Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_**
>> ROSETTA_REBUILD_1/RUN_1/**REBUILD_IN_SETS_1/RUN_1/WORK_**
>> 1/aligned_model.pdb
>> Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_**ROSETTA_REBUILD_1/RUN_1/**
>> REBUILD_IN_SETS_1/RUN_1/WORK_**1/rebuild.log
>>
>> **************ERROR ENDING**********************
>> Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_**
>> ROSETTA_REBUILD_1/RUN_1/**REBUILD_IN_SETS_1/RUN_1/WORK_**1/rebuild.log
>>
>>
>> The rebuild log had repeats of several errors that I am not sure how to
>> address:
>>
>> core.conformation.**Conformation: [ WARNING ] missing heavyatom:  CD2 on
>> residue PHE 3 (repeated several times)
>>
>> core.fragments.**ConstantLengthFragSet: line too short: Skipping line '
>> (repeated several times)
>>
>>
>> core.fragments.**ConstantLengthFragSet: finished reading top 0 0mer
>> fragments from file/dataFiles/aat000_03_05.**200_v1_3
>> protocols.loops.loops_main: Frag libraries debug none 1
>>
>>
>>
>>
>>
>>
>> ______________________________**_________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online.org/mailman/listinfo/phenixbb>
>>
>>
> --
>         Andreas Förster, Research Associate
>         Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>             http://www.msf.bio.ic.ac.uk
>
> ______________________________**_________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online.org/mailman/listinfo/phenixbb>
>
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