Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Errors in Getting Erraser to run
- This topic has 33 replies, 4 voices, and was last updated 7 years, 6 months ago by
Anonymous.
-
AuthorPosts
-
-
June 1, 2017 at 11:13 pm #2662
Anonymous
Hey there,
I’m having trouble getting erraser to run. The following command:
erraser.py -pdb model_real_space_refined.pdb -map ../maps/FFT_13/70S_converted_1.ccp4 -map_reso 3.73
Give the errors as seen in the attached output.txt.
Everything compiled fine, using gcc5.4
any help would be appreciated.
cheers
matt B
-
June 2, 2017 at 2:48 pm #12364
I’m pretty sure this is a bug with the RNA code using the wrong initialization calls (core init instead of protocols init or devel init). The first thing to try is to use a recent weekly release and see if that works. If not we’ll try to fix THAT one instead of trying to fix 3.7.
-
June 2, 2017 at 2:48 pm #12885
I’m pretty sure this is a bug with the RNA code using the wrong initialization calls (core init instead of protocols init or devel init). The first thing to try is to use a recent weekly release and see if that works. If not we’ll try to fix THAT one instead of trying to fix 3.7.
-
June 2, 2017 at 2:48 pm #13406
I’m pretty sure this is a bug with the RNA code using the wrong initialization calls (core init instead of protocols init or devel init). The first thing to try is to use a recent weekly release and see if that works. If not we’ll try to fix THAT one instead of trying to fix 3.7.
-
June 19, 2017 at 2:21 am #12421
Similar issues with the lastest build as well. See output below:
Also here is my .bashrc, as it appears in this instance its a path issue?
#Rosetta
export ROSETTA=/home/mbelouso/rosetta3.8
export PHENIX_ROSETTA_PATH=$ROSETTA
export PATH=$ROSETTA/main/source/bin:$PATH
export RNA_TOOLS=$ROSETTA/tools/rna_tools
export FRAGMENT_TOOLS=$ROSETTA/tools/fragment_tools
export ROSETTA3_DB=$ROSETTA/main/database
export ERRASER=$ROSETTA/main/source/src/apps/public/ERRASER
#export ERRASER=$ROSETTA/tools/ERRASER
export PATH=$ERRASER:$PATH
python $RNA_TOOLS/sym_link.py
export PATH=$RNA_TOOLS/bin:$PATH
export PATH=$FRAGMENT_TOOLS:$PATH
export PYTHONPATH=$PYTHONPATH:$RNA_TOOLS/bin/
erraser.py output:
erraser.py -pdb 70S_LinR2_Draft.pdb -map ../maps/FFT_13/70S_converted_1.ccp4 -map_reso 3.73
pdb = 70S_LinR2_Draft.pdb
map = ../maps/FFT_13/70S_converted_1.ccp4
out_pdb =
map_reso = 3.73
rna_prot_erraser = False
debug = False
rosetta_folder =
rosetta_bin =
rosetta_database =
nproc = 0
multiproc_minimize = False
guarantee_no_DNA = False
n_iterate = 1
rebuild_rmsd = True
rebuild_all = False
fixed_res = []
rebuild_extra_res = []
use_native_edensity_cutoff = False
constrain_chi = True
native_screen_RMSD = 3.0
search_syn_pyrimidine_only_when_native_syn = True
num_pose_kept = 100
num_pose_kept_cluster = 10
o2prime_legacy_mode = True
scoring_file =
use_2prime_OH_potential = False
fcc2012_new_torsional_potential = True
fcc2012_scoring_file = True
enlarge_H_lj = True
###################################
Starting erraser...
Create temporary directory /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/...
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 61, in erraser
rna_rosetta_ready_set('start.pdb', 'minimize_0.pdb', option, option.rosetta_bin, option.rosetta_database, option.rna_prot_erraser)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 358, in rna_rosetta_ready_set
command = rosetta_bin_path("erraser_minimizer", rosetta_bin)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 59, in rosetta_bin_path
check_path_exist(exe_path)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 653, in check_path_exist
error_exit("Path %s does not exist!" % path_name)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 32, in error_exit
raise ErraserError(message)
erraser_util.ErraserError: Path /home/mbelouso/rosetta3.8/main/source/bin/erraser_minimizerfailed_to_find_Rosetta_path does not exist!
-
June 19, 2017 at 2:21 am #12942
Similar issues with the lastest build as well. See output below:
Also here is my .bashrc, as it appears in this instance its a path issue?
#Rosetta
export ROSETTA=/home/mbelouso/rosetta3.8
export PHENIX_ROSETTA_PATH=$ROSETTA
export PATH=$ROSETTA/main/source/bin:$PATH
export RNA_TOOLS=$ROSETTA/tools/rna_tools
export FRAGMENT_TOOLS=$ROSETTA/tools/fragment_tools
export ROSETTA3_DB=$ROSETTA/main/database
export ERRASER=$ROSETTA/main/source/src/apps/public/ERRASER
#export ERRASER=$ROSETTA/tools/ERRASER
export PATH=$ERRASER:$PATH
python $RNA_TOOLS/sym_link.py
export PATH=$RNA_TOOLS/bin:$PATH
export PATH=$FRAGMENT_TOOLS:$PATH
export PYTHONPATH=$PYTHONPATH:$RNA_TOOLS/bin/
erraser.py output:
erraser.py -pdb 70S_LinR2_Draft.pdb -map ../maps/FFT_13/70S_converted_1.ccp4 -map_reso 3.73
pdb = 70S_LinR2_Draft.pdb
map = ../maps/FFT_13/70S_converted_1.ccp4
out_pdb =
map_reso = 3.73
rna_prot_erraser = False
debug = False
rosetta_folder =
rosetta_bin =
rosetta_database =
nproc = 0
multiproc_minimize = False
guarantee_no_DNA = False
n_iterate = 1
rebuild_rmsd = True
rebuild_all = False
fixed_res = []
rebuild_extra_res = []
use_native_edensity_cutoff = False
constrain_chi = True
native_screen_RMSD = 3.0
search_syn_pyrimidine_only_when_native_syn = True
num_pose_kept = 100
num_pose_kept_cluster = 10
o2prime_legacy_mode = True
scoring_file =
use_2prime_OH_potential = False
fcc2012_new_torsional_potential = True
fcc2012_scoring_file = True
enlarge_H_lj = True
###################################
Starting erraser...
Create temporary directory /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/...
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 61, in erraser
rna_rosetta_ready_set('start.pdb', 'minimize_0.pdb', option, option.rosetta_bin, option.rosetta_database, option.rna_prot_erraser)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 358, in rna_rosetta_ready_set
command = rosetta_bin_path("erraser_minimizer", rosetta_bin)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 59, in rosetta_bin_path
check_path_exist(exe_path)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 653, in check_path_exist
error_exit("Path %s does not exist!" % path_name)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 32, in error_exit
raise ErraserError(message)
erraser_util.ErraserError: Path /home/mbelouso/rosetta3.8/main/source/bin/erraser_minimizerfailed_to_find_Rosetta_path does not exist!
-
June 19, 2017 at 2:21 am #13463
Similar issues with the lastest build as well. See output below:
Also here is my .bashrc, as it appears in this instance its a path issue?
#Rosetta
export ROSETTA=/home/mbelouso/rosetta3.8
export PHENIX_ROSETTA_PATH=$ROSETTA
export PATH=$ROSETTA/main/source/bin:$PATH
export RNA_TOOLS=$ROSETTA/tools/rna_tools
export FRAGMENT_TOOLS=$ROSETTA/tools/fragment_tools
export ROSETTA3_DB=$ROSETTA/main/database
export ERRASER=$ROSETTA/main/source/src/apps/public/ERRASER
#export ERRASER=$ROSETTA/tools/ERRASER
export PATH=$ERRASER:$PATH
python $RNA_TOOLS/sym_link.py
export PATH=$RNA_TOOLS/bin:$PATH
export PATH=$FRAGMENT_TOOLS:$PATH
export PYTHONPATH=$PYTHONPATH:$RNA_TOOLS/bin/
erraser.py output:
erraser.py -pdb 70S_LinR2_Draft.pdb -map ../maps/FFT_13/70S_converted_1.ccp4 -map_reso 3.73
pdb = 70S_LinR2_Draft.pdb
map = ../maps/FFT_13/70S_converted_1.ccp4
out_pdb =
map_reso = 3.73
rna_prot_erraser = False
debug = False
rosetta_folder =
rosetta_bin =
rosetta_database =
nproc = 0
multiproc_minimize = False
guarantee_no_DNA = False
n_iterate = 1
rebuild_rmsd = True
rebuild_all = False
fixed_res = []
rebuild_extra_res = []
use_native_edensity_cutoff = False
constrain_chi = True
native_screen_RMSD = 3.0
search_syn_pyrimidine_only_when_native_syn = True
num_pose_kept = 100
num_pose_kept_cluster = 10
o2prime_legacy_mode = True
scoring_file =
use_2prime_OH_potential = False
fcc2012_new_torsional_potential = True
fcc2012_scoring_file = True
enlarge_H_lj = True
###################################
Starting erraser...
Create temporary directory /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/...
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 61, in erraser
rna_rosetta_ready_set('start.pdb', 'minimize_0.pdb', option, option.rosetta_bin, option.rosetta_database, option.rna_prot_erraser)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 358, in rna_rosetta_ready_set
command = rosetta_bin_path("erraser_minimizer", rosetta_bin)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 59, in rosetta_bin_path
check_path_exist(exe_path)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 653, in check_path_exist
error_exit("Path %s does not exist!" % path_name)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 32, in error_exit
raise ErraserError(message)
erraser_util.ErraserError: Path /home/mbelouso/rosetta3.8/main/source/bin/erraser_minimizerfailed_to_find_Rosetta_path does not exist!
-
June 19, 2017 at 11:25 pm #12423
Still not working:
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 609, in seq_rebuild_new
rna_swa_test_exe = rosetta_bin_path("resample_full_model", option.rosetta_bin )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 59, in rosetta_bin_path
check_path_exist(exe_path)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 653, in check_path_exist
error_exit("Path %s does not exist!" % path_name)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 32, in error_exit
raise ErraserError(message)
erraser_util.ErraserError: Path /home/mbelouso/rosetta3.8/main/source/bin/resample_full_modelfailed_to_find_Rosetta_path does not exist!So went and made another symlink for resample_full_model
Then these errors occured (see attached txt file for output).
Is there something critical that I have missed in setting things up?
-
June 19, 2017 at 11:25 pm #12944
Still not working:
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 609, in seq_rebuild_new
rna_swa_test_exe = rosetta_bin_path("resample_full_model", option.rosetta_bin )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 59, in rosetta_bin_path
check_path_exist(exe_path)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 653, in check_path_exist
error_exit("Path %s does not exist!" % path_name)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 32, in error_exit
raise ErraserError(message)
erraser_util.ErraserError: Path /home/mbelouso/rosetta3.8/main/source/bin/resample_full_modelfailed_to_find_Rosetta_path does not exist!So went and made another symlink for resample_full_model
Then these errors occured (see attached txt file for output).
Is there something critical that I have missed in setting things up?
-
June 19, 2017 at 11:25 pm #13465
Still not working:
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 609, in seq_rebuild_new
rna_swa_test_exe = rosetta_bin_path("resample_full_model", option.rosetta_bin )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 59, in rosetta_bin_path
check_path_exist(exe_path)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 653, in check_path_exist
error_exit("Path %s does not exist!" % path_name)
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 32, in error_exit
raise ErraserError(message)
erraser_util.ErraserError: Path /home/mbelouso/rosetta3.8/main/source/bin/resample_full_modelfailed_to_find_Rosetta_path does not exist!So went and made another symlink for resample_full_model
Then these errors occured (see attached txt file for output).
Is there something critical that I have missed in setting things up?
-
June 23, 2017 at 3:48 pm #13486
There’s an ‘INSTALL’ script in the rna_tools subdirectory tools repo. Try typing `source tools/rna_tools/INSTALL` (and consider adding it to your .bashrc). That should fix your PYTHONPATH so it finds parse_tag, and pdb2fasta is more likely to work.
The hacky way is to manually edit that fasta file so that it says what it ‘should say’ but that is likely to help you for one step of the protocol and then fall apart a little thereafter.
-
June 26, 2017 at 11:02 am #13495
Maybe. Hard to say without more than just the backtrace, but maybe it isn’t finding resample_full_model or swa_rna_main the same way it wasn’t finding erraser_minimizer.
I can try to run it myself, if you would feel comfortable sharing the data (privately; I can give you my email); that might help debug faster.
-
June 19, 2017 at 4:44 am #12422
Ok…. So I fixed the launching problem by going into:
$ROSETTA/main/source/bin and just making a symbolic link to erraser_minimizer
ln -s erraser_minimizer.linuxgccrelease erraser_minimizerSeems to at least start now. Seems like a bug in erraser_util.py
-
June 19, 2017 at 4:44 am #12943
Ok…. So I fixed the launching problem by going into:
$ROSETTA/main/source/bin and just making a symbolic link to erraser_minimizer
ln -s erraser_minimizer.linuxgccrelease erraser_minimizerSeems to at least start now. Seems like a bug in erraser_util.py
-
June 19, 2017 at 4:44 am #13464
Ok…. So I fixed the launching problem by going into:
$ROSETTA/main/source/bin and just making a symbolic link to erraser_minimizer
ln -s erraser_minimizer.linuxgccrelease erraser_minimizerSeems to at least start now. Seems like a bug in erraser_util.py
-
June 20, 2017 at 5:09 pm #12429
No, not really.
The lab that maintains ERRASER uses a slightly different build system than the standard Scons build system. They’ve customized this build system such that it also produces non-labled executables. (So they get a `main/source/bin/resample_full_model` in addtion to the `main/source/bin/resample_full_model.linuxgccrelease` or the `main/source/bin/resample_full_model.macclangrelease` executables.) When they set up the erraser running scripts, they apparently forgot that not everyone is using that build system, and so are using the unlabeled executable names, rather than the labeled ones that the Scons build system produces.
Doing the symlinking as you’re doing is a reasonable way of handling the issue.
-
June 20, 2017 at 5:09 pm #12950
No, not really.
The lab that maintains ERRASER uses a slightly different build system than the standard Scons build system. They’ve customized this build system such that it also produces non-labled executables. (So they get a `main/source/bin/resample_full_model` in addtion to the `main/source/bin/resample_full_model.linuxgccrelease` or the `main/source/bin/resample_full_model.macclangrelease` executables.) When they set up the erraser running scripts, they apparently forgot that not everyone is using that build system, and so are using the unlabeled executable names, rather than the labeled ones that the Scons build system produces.
Doing the symlinking as you’re doing is a reasonable way of handling the issue.
-
June 20, 2017 at 5:09 pm #13471
No, not really.
The lab that maintains ERRASER uses a slightly different build system than the standard Scons build system. They’ve customized this build system such that it also produces non-labled executables. (So they get a `main/source/bin/resample_full_model` in addtion to the `main/source/bin/resample_full_model.linuxgccrelease` or the `main/source/bin/resample_full_model.macclangrelease` executables.) When they set up the erraser running scripts, they apparently forgot that not everyone is using that build system, and so are using the unlabeled executable names, rather than the labeled ones that the Scons build system produces.
Doing the symlinking as you’re doing is a reasonable way of handling the issue.
-
June 21, 2017 at 3:03 am #12430
Hey, so if this is the case that this should be built in a different way, is there some documentation I can follow? Because I’m a bit stuck trying to fix the error below. Seems like the python script is trying to find something that isn’t there? A module called, parse_tag.
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/tools/rna_tools/bin/pdb2fasta.py", line 6, in <module>
from get_sequence import get_sequences
File "/home/mbelouso/rosetta3.8/tools/rna_tools/pdb_util/get_sequence.py", line 5, in <module>
from parse_tag import parse_tag
ImportError: No module named parse_tag
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.8/main/source/bin/resample_full_model -s -
June 21, 2017 at 3:03 am #12951
Hey, so if this is the case that this should be built in a different way, is there some documentation I can follow? Because I’m a bit stuck trying to fix the error below. Seems like the python script is trying to find something that isn’t there? A module called, parse_tag.
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/tools/rna_tools/bin/pdb2fasta.py", line 6, in <module>
from get_sequence import get_sequences
File "/home/mbelouso/rosetta3.8/tools/rna_tools/pdb_util/get_sequence.py", line 5, in <module>
from parse_tag import parse_tag
ImportError: No module named parse_tag
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.8/main/source/bin/resample_full_model -s -
June 21, 2017 at 3:03 am #13472
Hey, so if this is the case that this should be built in a different way, is there some documentation I can follow? Because I’m a bit stuck trying to fix the error below. Seems like the python script is trying to find something that isn’t there? A module called, parse_tag.
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/tools/rna_tools/bin/pdb2fasta.py", line 6, in <module>
from get_sequence import get_sequences
File "/home/mbelouso/rosetta3.8/tools/rna_tools/pdb_util/get_sequence.py", line 5, in <module>
from parse_tag import parse_tag
ImportError: No module named parse_tag
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.8/main/source/bin/resample_full_model -s -
June 21, 2017 at 7:15 pm #12433
Try going to main/source/src/apps/public/ERRASER/erraser_util.py line 52 or so, and add a dot to the beginning of “linuxgccrelease”, like it is with linuxclangrelease, macosgccrelease and macosclangrelease.
-
June 21, 2017 at 7:15 pm #12954
Try going to main/source/src/apps/public/ERRASER/erraser_util.py line 52 or so, and add a dot to the beginning of “linuxgccrelease”, like it is with linuxclangrelease, macosgccrelease and macosclangrelease.
-
June 21, 2017 at 7:15 pm #13475
Try going to main/source/src/apps/public/ERRASER/erraser_util.py line 52 or so, and add a dot to the beginning of “linuxgccrelease”, like it is with linuxclangrelease, macosgccrelease and macosclangrelease.
-
June 22, 2017 at 12:07 am #12436
So adding the dot did help to the erraser_util.py script. But now this error…..
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 737, in seq_rebuild_new
subprocess.call(["pdb2fasta.py", SWA_option.input_pdb ], stdout=out ) #, ">", fasta_file ])
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 168, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 390, in __init__
errread, errwrite)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directorySo then I put the following in my environment variables, as it clearly wanted the right pdb2fasta.py
export PDBTOOLS=$ROSETTA/main/source/scripts/python/public
export PATH=$PDBTOOLS:$PATH
export PYTHONPATH=$PYTHONPATH:$PDBTOOLSand then got this error:
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.8/main/source/bin/resample_full_model.linuxgccrelease -s /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/minimize_1.pdb -fasta /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/minimize_1_seq_rebuild_temp//fasta -ignore_zero_occupancy false -out:file:silent blah.out -output_virtual true -rm_virt_phosphate true -sampler_extra_chi_rotamer true -cluster::radius 0.3 -stepwise:rna:centroid_screen true -sampler_allow_syn_pyrimidine true -minimize_and_score_native_pose false -native_edensity_score_cutoff -1 -rmsd_screen 3.0 -sampler_num_pose_kept 100 -PBP_clustering_at_chain_closure true -allow_chain_boundary_jump_partner_right_at_fixed_BP true -allow_virtual_side_chains false -sampler_perform_phosphate_pack false -add_virt_root true -sample_res A:100........Now, i’m completely stuck again…..
-
June 22, 2017 at 12:07 am #12957
So adding the dot did help to the erraser_util.py script. But now this error…..
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 737, in seq_rebuild_new
subprocess.call(["pdb2fasta.py", SWA_option.input_pdb ], stdout=out ) #, ">", fasta_file ])
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 168, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 390, in __init__
errread, errwrite)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directorySo then I put the following in my environment variables, as it clearly wanted the right pdb2fasta.py
export PDBTOOLS=$ROSETTA/main/source/scripts/python/public
export PATH=$PDBTOOLS:$PATH
export PYTHONPATH=$PYTHONPATH:$PDBTOOLSand then got this error:
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.8/main/source/bin/resample_full_model.linuxgccrelease -s /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/minimize_1.pdb -fasta /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/minimize_1_seq_rebuild_temp//fasta -ignore_zero_occupancy false -out:file:silent blah.out -output_virtual true -rm_virt_phosphate true -sampler_extra_chi_rotamer true -cluster::radius 0.3 -stepwise:rna:centroid_screen true -sampler_allow_syn_pyrimidine true -minimize_and_score_native_pose false -native_edensity_score_cutoff -1 -rmsd_screen 3.0 -sampler_num_pose_kept 100 -PBP_clustering_at_chain_closure true -allow_chain_boundary_jump_partner_right_at_fixed_BP true -allow_virtual_side_chains false -sampler_perform_phosphate_pack false -add_virt_root true -sample_res A:100........Now, i’m completely stuck again…..
-
June 22, 2017 at 12:07 am #13478
So adding the dot did help to the erraser_util.py script. But now this error…..
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 737, in seq_rebuild_new
subprocess.call(["pdb2fasta.py", SWA_option.input_pdb ], stdout=out ) #, ">", fasta_file ])
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 168, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 390, in __init__
errread, errwrite)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directorySo then I put the following in my environment variables, as it clearly wanted the right pdb2fasta.py
export PDBTOOLS=$ROSETTA/main/source/scripts/python/public
export PATH=$PDBTOOLS:$PATH
export PYTHONPATH=$PYTHONPATH:$PDBTOOLSand then got this error:
Traceback (most recent call last):
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/mbelouso/rosetta3.8/main/source/bin/resample_full_model.linuxgccrelease -s /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/minimize_1.pdb -fasta /home/mbelouso/l1/EM/VRE/LinR2_Faecalis/70S/realspace04/70S_LinR2_Draft_erraser_temp/minimize_1_seq_rebuild_temp//fasta -ignore_zero_occupancy false -out:file:silent blah.out -output_virtual true -rm_virt_phosphate true -sampler_extra_chi_rotamer true -cluster::radius 0.3 -stepwise:rna:centroid_screen true -sampler_allow_syn_pyrimidine true -minimize_and_score_native_pose false -native_edensity_score_cutoff -1 -rmsd_screen 3.0 -sampler_num_pose_kept 100 -PBP_clustering_at_chain_closure true -allow_chain_boundary_jump_partner_right_at_fixed_BP true -allow_virtual_side_chains false -sampler_perform_phosphate_pack false -add_virt_root true -sample_res A:100........Now, i’m completely stuck again…..
-
June 22, 2017 at 4:55 pm #12437
Can you check the ‘seq_rebuild.out’ and ‘seq_rebuild.err’ files to see what error messages are being printed there?
-
June 22, 2017 at 4:55 pm #12958
Can you check the ‘seq_rebuild.out’ and ‘seq_rebuild.err’ files to see what error messages are being printed there?
-
June 22, 2017 at 4:55 pm #13479
Can you check the ‘seq_rebuild.out’ and ‘seq_rebuild.err’ files to see what error messages are being printed there?
-
June 22, 2017 at 11:42 pm #13481
-
June 22, 2017 at 11:52 pm #13482
To follow up on this, I think the problem is still the pdb2fasta.py as the fasta file in the rebuild directory is just full of XXXXXXXX with no sequence data. So perhaps I need to point to a different pdb2fasta.py in my environment variables?
-
June 25, 2017 at 11:56 pm #13494
Hey so I sourced that INSTALL script.
Similar problem:
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser.py", line 23, in <module>
erraser( option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 166, in erraser
outlier_rebuild_if_necessary( step, rebuild_res_error, rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 212, in outlier_rebuild_if_necessary
seq_rebuild_new( rebuild_option )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 808, in seq_rebuild_new
subprocess_call( command, 'seq_rebuild.out', 'seq_rebuild.err' )
File "/home/mbelouso/rosetta3.8/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call
subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)
File "/usr/local/phenix-1.12rc0-2787/base/lib/python2.7/subprocess.py", line 186, in check_call
raise CalledProcessError(retcode, cmd)
Maybe something is up with the version of Phenix installed?
-
June 26, 2017 at 11:46 pm #13501
Sounds great! Please email me on matthew.belousoff@monash.edu
I’m pretty sure its finding resample_full_model, and the issue lies somewhere in the pdb2fasta.py as it still spits out a meaningless fasta file (full of X instead of residue identifiers).
cheers!
matt B
-
-
AuthorPosts
- You must be logged in to reply to this topic.