[phenixbb] Trouble running getting ERRASER to run

Mon Apr 16 14:38:33 PDT 2018

Shintaro

The ERRASER interface is a little broken. We are working on it and will
make an announcement when it's fixed.

Sorry.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Mon, Apr 16, 2018 at 12:42 PM, Shintaro Aibara <
shintaro.aibara at scilifelab.se> wrote:

> *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<char, std::char_traits<char>,
> std::allocator<char> > 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<unsigned long,
> std::less<unsigned long>, std::allocator<unsigned long> > 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_ptr<protocols::moves::Mover>&,
> long, std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >&, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >&, 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_ptr<protocols::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_ptr<protocols::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
>
>
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