[phenixbb] Trouble running getting ERRASER to run

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Tue Apr 17 09:55:46 PDT 2018 

I used Erraser fairly recently in Phenix 1.12_2829 using the command line.
It worked fine from the command line, but I also had no success from the
GUI.

Good luck

Ursula

On Tue, Apr 17, 2018 at 2:16 AM, Shintaro Aibara <
shintaro.aibara at scilifelab.se> wrote:

> Hi Nigel,
>
> Thanks for letting me know. Are there any previous versions of
> Phenix/Rosetta that are known to work? I remember getting it to run on OSX
> in the past at some point....It would be great if I could run some jobs
> even if it means running it through the command-line
>
> Best wishes,
> Shintaro
>
> On Mon, Apr 16, 2018 at 11:38 PM, Nigel Moriarty <nwmoriarty at lbl.gov>
> wrote:
>
>> 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_2018.09.600
>>> 72_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_2018.09.600
>>> 72_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_2018.09.600
>>> 72_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_2018.09.600
>>> 72_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_2018.09.600
>>> 72_bundle/main/source/build/src/release/linux/4.15/64/x86/
>>> gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistri
>>> butor::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_2018.09.600
>>> 72_bundle/main/source/build/src/release/linux/4.15/64/x86/
>>> gcc/5.4/default/libprotocols.1.so(protocols::jd2::JobDistri
>>> butor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x166)
>>> [0x7f3e344cedc6]
>>> /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600
>>> 72_bundle/main/source/build/src/release/linux/4.15/64/x86/
>>> gcc/5.4/default/libprotocols.1.so(protocols::jd2::FileSyste
>>> mJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57)
>>> [0x7f3e344b4d67]
>>> /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600
>>> 72_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x40480e]
>>> /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.600
>>> 72_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_2018.09.600
>>> 72_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4045b9]
>>> Traceback (most recent call last):
>>>   File "/home/saibara/software/phenix/phenix-dev-3092/build/../modu
>>> les/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_2018.09.60
>>> 072_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_2018.09.60
>>> 072_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_2018.09.60
>>> 072_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/rosett
>>> a/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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>>>
>>
>>
>
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-- 
Ursula Schulze-Gahmen, Ph.D.
Project Scientist
UC Berkeley, QB3
360 Stanley Hall #3220
Berkeley, CA 94720-3220
(510) 643 9491
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