[phenixbb] Trouble running getting ERRASER to run

Shintaro Aibara shintaro.aibara at scilifelab.se
Tue Apr 17 02:16:27 PDT 2018 

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.
>> 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::Job
>> Distributor::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::Job
>> Distributor::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::Fil
>> eSystemJobDistributor::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/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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