*Dear PhenixBB,*
*I am trying to get ERRASER to run and am struggling a bit. I was wondering
if somebody could point me in the right way. Apologies if this has been
asked before - my Google-Fu is inadequate.*
*Phenix Version: dev-3092*
*Rosetta Version: 2018.09.60072*
*I built rosetta using scons as per the instructions online and fired
rosetta.build_phenix_interface with no errors. I've identified that the
erraser directory lives in main/source/src/apps/public/ERRASER and
accordingly set my environmental variables.*
*Being fairly clunky around the linux environment, I am probably doing
something very silly. Any help would be much appreciated.*
*Best wishes,*
*Shintaro*
*When I try to run erraser from the phenix GUI I am greeted by this error
message:*
TypeError : __init__() takes at least 3 arguments (1 given)
Traceback (most recent call last):
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/App.py",
line 784, in OnTimer
self.run_manager.update(update_backgrounded=False)
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py",
line 213, in update
process.update()
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py",
line 136, in update
self._process.update()
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/runtime_utils.py",
line 306, in update
(error, traceback_info) = easy_pickle.load(self.error_file)
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/easy_pickle.py",
line 80, in load
return cPickle.loads(_open(file_name, "rb").read())
TypeError: __init__() takes at least 3 arguments (1 given)
*Alternatively if I try to fire phenix.erraser through the command line, I
get something like this:*
Running ERRASER Rosetta app...
###################################
Path to ERRASER:
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER
ERROR: Assertion `scorefxn_->get_weight( cart_bonded ) > 0` failed.
ERROR:: Exit from: src/protocols/rna/movers/ErraserMinimizerMover.cc line:
238
BACKTRACE:
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libutility.so(utility::exit(char
const*, int, std::__cxx11::basic_string const&, int)+0x2ea) [0x7f3e2b7798fa]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/
libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(core::chemical::ResidueType
const&, unsigned long const&)+0x92) [0x7f3e34c17062]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/
libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(core::kinematics::MoveMap&,
core::pose::Pose&, ObjexxFCL::FArray1D<bool>&, std::set const&)+0x20a)
[0x7f3e34c1771a]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/
libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::apply(core::pose::Pose&)+0x2020)
[0x7f3e34c20f70]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/
libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptrprotocols::moves::Mover&,
long, std::__cxx11::basic_string&, std::__cxx11::basic_string&, unsigned long&, unsigned
long&, bool)+0xbed) [0x7f3e344cc9bd]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/
libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptrprotocols::moves::Mover)+0x166)
[0x7f3e344cedc6]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/
libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptrprotocols::moves::Mover)+0x57)
[0x7f3e344b4d67]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease()
[0x40480e]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease()
[0x4037b1]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f3e32bdc830]
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease()
[0x4045b9]
Traceback (most recent call last):
File
"/home/saibara/software/phenix/phenix-dev-3092/build/../modules/phenix/phenix/command_line/erraser.py",
line 14, in <module>
erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:])
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py",
line 349, in __init__
self.run(params,out=out)
File
"/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py",
line 459, in run
erraser(option)
File
"/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py",
line 99, in erraser
erraser_minimize( minimize_option ) #full_struct_slice_and_minimize(
minimize_option )
File
"/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py",
line 478, in erraser_minimize
subprocess_call(command, sys.stdout, sys.stderr)
File
"/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/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
"/home/saibara/software/phenix/phenix-dev-3092/base/lib/python2.7/subprocess.py",
line 186, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command
'/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease
-database
/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/database/
-s
/home/saibara/Phenix/hsmitoribo_drug/rnaonly_erraser_temp/minimize_0.pdb
-score:weights stepwise/rna/rna_hires_elec_dens_FCC2012
-score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo
true -rna::erraser::rna_prot_erraser false -rna::vary_geometry true
-constrain_P true -attempt_pyrimidine_flip false
-rna::erraser::skip_minimize false -chemical:enlarge_H_lj false
-in:guarantee_no_DNA false -out:file:write_pdb_link_records true -scale_d
100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true
-use_2prime_OH_potential false -edensity:mapfile
/home/saibara/Phenix/hsmitoribo_drug/cheatmap.ccp4 -edensity:mapreso 3.0
-edensity:realign no -graphics false -skip_connect_info true ' returned
non-zero exit status 255
