[phenixbb] Problems with rosetta_mr
Yoni Haitin
haitinyo at uw.edu
Fri Dec 21 08:54:48 PST 2012
Hello all,
I have been trying (desperetly) to run the Rosetta_MR.
I have encountered some problems with my data, so I switched to the "HNP3-mr-rosetta" tutorial dataset.
I followd the debugging suggestions in the instructions webpage with no improvement. It seems that I have a problem in the rebuild stage.
Attached are the RUN_FILE_1.log from REBUILD_IN_SETS_5 and ../WORK_1/rebuild.log. The edited_align.ali file cannot be opened for some reason.
Another issue is that the map used is being taken from "overall_best_denmod_map_coeffs_nf.map" instead of "cycle_best" (as is in the tutorial's mr_rosetta_output log). this seems to produce an error (last log file attached).
What should I do next?
Thank you,
Yoni
Parameters taken from: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/PARAMS_1.eff
# mr_rosetta_rebuild
#
# Run automr mr_rosetta_rebuild with rosetta
# Type phenix.doc for help
Values of all params:
mr_rosetta_rebuild {
input_files {
model = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb"
map = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map"
seq_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/EDITED_1dfn.seq"
hhr_files = None
alignment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali"
model_info_file = ""
fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_09_05.200_v1_3.gz"
fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_03_05.200_v1_3.gz"
fragment_files_chain_list = None
fragment_files_9_mer_by_chain = None
fragment_files_3_mer_by_chain = None
use_dummy_fragment_files = False
sort_fragment_files = True
}
output_files {
log = "mr_rosetta_rebuild.log"
params_out = "mr_rosetta_rebuild_params.eff"
}
directories {
temp_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1"
workdir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1"
output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1"
gui_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta"
top_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14"
rosetta_path = "/Users/administrator/rosetta_3.4"
rosetta_binary_dir = "rosetta_source/bin"
rosetta_binary_name = "mr_protocols.default.macosgccrelease"
rosetta_script_dir = "rosetta_source/src/apps/public/electron_density"
rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/"
rosetta_database_dir = "rosetta_database"
}
rosetta_rebuild {
run_rosetta_rebuild = True
stage_to_rebuild = "rescored_mr_solution"
max_solutions_to_rebuild = 5
min_solutions_to_rebuild = 1
llg_percent_of_max_to_keep = 50
rosetta_models = 20
chunk_size = 1
edit_model = True
superpose_model = False
}
rosetta_modeling {
map_resolution = 3
map_grid_spacing = 1.5
map_weight = 1
map_window = 5
include_solvation_energy = True
weights_file = ""
}
crystal_info {
resolution = 0
space_group = "P 21 21 2"
chain_type = *PROTEIN DNA RNA
ncs_copies = 1
}
control {
verbose = False
debug = False
raise_sorry = False
dry_run = False
nproc = 1
group_run_command = "sh "
queue_commands = None
condor_universe = "vanilla"
add_double_quotes_in_condor = True
condor = None
one_subprocess_level = None
single_run_command = "sh "
last_process_is_local = True
background = True
ignore_errors_in_subprocess = True
check_run_command = False
max_wait_time = 100
wait_between_submit_time = 1
wizard_directory_number = 14
n_dir_max = 100000
number_to_print = 5
write_run_directory_to_file = "/Users/administrator/Yoni/Rosettal
tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/INFO_FILE_1"
resolve_command_list = None
start_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \
similarity refine_top_models average_density_top_models \
relax_top_models autobuild_top_models \
setup_repeat_mr_rosetta repeat_mr_rosetta
stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \
similarity refine_top_models average_density_top_models \
relax_top_models autobuild_top_models \
setup_repeat_mr_rosetta repeat_mr_rosetta
clean_up = False
}
non_user_params {
file_base = "1zmm_mr.1"
print_citations = False
highest_id = 10
is_sub_process = True
dummy_autobuild = False
dummy_refinement = False
dummy_rosetta = False
prerefine_only = False
skip_clash_guard = True
correct_special_position_tolerance = None
comparison_mtz = ""
labin_comparison_mtz = None
write_local_files = False
rosetta_fixed_seed = None
}
}
Starting mr_rosetta_rebuild
Date: Thu Dec 20 14:44:49 2012
Directory: /Users/administrator/Yoni/Rosettal tutorial
data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5
HOST = ZagottasMacPro.local
HOSTTYPE = intel-mac
MACHTYPE = x86_64
OSTYPE = darwin
VENDOR = apple
USER = administrator
PID = 36828
Checking rosetta paths:
rosetta binary:
/Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease
database_dir: /Users/administrator/rosetta_3.4/rosetta_database
script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/public/electron_density
pilot_script_dir:
/Users/administrator/rosetta_3.4/rosetta_source/src/apps/pilot/frank/
Changing to work directory: /Users/administrator/Yoni/Rosettal
tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1
Rebuilding the model /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb
with rosetta
Rebuilding model using map at resolution of 3.0 A
Generating 20 rebuilt models
================================================================================
Reading model from /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb
================================================================================
ALIGNMENT LINES:
## TARGET 1zmm_
# hhsearch
scores_from_program: 0 1.00
0 DCYCRIPACIAGERRYGTCIYQGRLWAFCC
1 -CYCRIPACIAGERRYGTCIYQGRLWAFCC
--
Trying to adjust the PDB sequence from alignment file:
-CYCRIPACIAGERRYGTCIYQGRLWAFCC
to match the actual PDB sequence:
YCRIPACIAGERRYGTCIYQGRLWAFCC
New alignment line 4 for PDB:
1 --YCRIPACIAGERRYGTCIYQGRLWAFCC
Start position of target sequence in sequence file: 0
Aligned model for comparison: /Users/administrator/Yoni/Rosettal
tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/aligned_model.pdb
Log for rebuilding: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log
**************ERROR ENDING********************** Failed to run REBUILD...see log file in /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log
**************ERROR ENDING**********************
---
Here is ../WORK_1/rebuild.log:
core.init: Mini-Rosetta version unknown from unknown
core.init: command:
/Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease
@rebuild.flags
core.init: 'RNG device' seed mode, using '/dev/urandom',
seed=345021854 seed_offset=0 real_seed=345021854
core.init.random: RandomGenerator:init: Normal mode, seed=345021854
RG_type=mt19937
ERROR: Warning: can't open file /Users/administrator/Yoni/Rosettal/
tutorial/ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali!
ERROR:: Exit from: src/core/sequence/util.cc line: 380
---
core.init: Mini-Rosetta version exported from unknown
core.init: command:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_source/bin/mr_protocols.default.macosgccrelease
@rebuild.flags
core.init: 'RNG device' seed mode, using '/dev/urandom',
seed=-340184367 seed_offset=0 real_seed=-340184367
core.init.random: RandomGenerator:init: Normal mode, seed=-340184367
RG_type=mt19937
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pdb_pair_stats_fine
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_n
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_pp
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/env_log.txt
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cbeta_den.txt
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pair_log.txt
core.io.database: Database file opened:
/Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cenpack_log.txt
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map /Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map.
Not loading map.
core.scoring.electron_density.ElectronDensity: [ ERROR ] Error loading density map named '/Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map'
--
Yoni Haitin, Ph.D.
Department of Physiology and Biophysics
University of Washington
Seattle, WA 98195-7290
Email: yonihaitin at gmail.com
Email(2): haitinyo at uw.edu
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