<div dir="ltr">Hi Nigel,<div><br></div><div>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</div><div><br></div><div>Best wishes,</div><div>Shintaro</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 16, 2018 at 11:38 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Shintaro<div><br></div><div>The ERRASER interface is a little broken. We are working on it and will make an announcement when it's fixed.</div><div><br></div><div>Sorry.</div></div><div class="gmail_extra"><br clear="all"><div><div class="m_8232461048087332639gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote"><div><div class="h5">On Mon, Apr 16, 2018 at 12:42 PM, Shintaro Aibara <span dir="ltr"><<a href="mailto:shintaro.aibara@scilifelab.se" target="_blank">shintaro.aibara@scilifelab.se</a><wbr>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><b>Dear PhenixBB,</b><div><b><br></b></div><div><b>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.</b></div><div><b><br></b></div><div><b>Phenix Version: dev-3092</b></div><div><b>Rosetta Version: 2018.09.60072</b></div><div><b><br></b></div><div><b>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/ER<wbr>RASER and accordingly set my environmental variables.</b></div><div><b><br></b></div><div><b>Being fairly clunky around the linux environment, I am probably doing something very silly. Any help would be much appreciated.</b></div><div><b><br></b></div><div><b>Best wishes,</b></div><div><b>Shintaro</b></div><div><b><br></b></div><div><b>When I try to run erraser from the phenix GUI I am greeted by this error message:</b></div><div><div><br></div><div>TypeError : __init__() takes at least 3 arguments (1 given)</div><div><br></div><div>Traceback (most recent call last):</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>phenix/wxGUI2/App.py", line 784, in OnTimer</div><div> self.run_manager.update(update<wbr>_backgrounded=False)</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>phenix/wxGUI2/ProcessControl.<wbr>py", line 213, in update</div><div> process.update()</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>phenix/wxGUI2/ProcessControl.<wbr>py", line 136, in update</div><div> self._process.update()</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>cctbx_project/libtbx/runtime_<wbr>utils.py", line 306, in update</div><div> (error, traceback_info) = easy_pickle.load(self.error_fi<wbr>le)</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>cctbx_project/libtbx/easy_<wbr>pickle.py", line 80, in load</div><div> return cPickle.loads(_open(file_name, "rb").read())</div><div>TypeError: __init__() takes at least 3 arguments (1 given)</div></div><div><br></div><div><br></div><div><b>Alternatively if I try to fire phenix.erraser through the command line, I get something like this:</b></div><div><br></div><div><div>Running ERRASER Rosetta app...</div><div>##############################<wbr>#####</div><div>Path to ERRASER: /home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/src/<wbr>apps/public/ERRASER</div><div><br></div><div>ERROR: Assertion `scorefxn_->get_weight( cart_bonded ) > 0` failed.</div><div>ERROR:: Exit from: src/protocols/rna/movers/Erras<wbr>erMinimizerMover.cc line: 238</div><div>BACKTRACE:</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<wbr>libutility.so(utility::exit(<wbr>char const*, int, std::__cxx11::basic_string<cha<wbr>r, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x7f3e2b7798fa]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<a href="http://libprotocols_d.6.so" target="_blank">libprot<wbr>ocols_d.6.so</a>(protocols::rna::<wbr>movers::ErraserMinimizerMover:<wbr>:i_want_this_atom_to_move(<wbr>core::chemical::ResidueType const&, unsigned long const&)+0x92) [0x7f3e34c17062]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<a href="http://libprotocols_d.6.so" target="_blank">libprot<wbr>ocols_d.6.so</a>(protocols::rna::<wbr>movers::ErraserMinimizerMover:<wbr>:vary_bond_geometry(core::kine<wbr>matics::MoveMap&, core::pose::Pose&, ObjexxFCL::FArray1D<bool>&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&)+0x20a) [0x7f3e34c1771a]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<a href="http://libprotocols_d.6.so" target="_blank">libprot<wbr>ocols_d.6.so</a>(protocols::rna::<wbr>movers::ErraserMinimizerMover:<wbr>:apply(core::pose::Pose&)+<wbr>0x2020) [0x7f3e34c20f70]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<a href="http://libprotocols.1.so" target="_blank">libprot<wbr>ocols.1.so</a>(protocols::jd2::Job<wbr>Distributor::run_one_job(std::<wbr>shared_ptr<protocols::moves::<wbr>Mover>&, long, std::__cxx11::basic_string<cha<wbr>r, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<cha<wbr>r, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbed) [0x7f3e344cc9bd]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<a href="http://libprotocols.1.so" target="_blank">libprot<wbr>ocols.1.so</a>(protocols::jd2::Job<wbr>Distributor::go_main(std::shar<wbr>ed_ptr<protocols::moves::Mover<wbr>>)+0x166) [0x7f3e344cedc6]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/<wbr>build/src/release/linux/4.15/<wbr>64/x86/gcc/5.4/default/<a href="http://libprotocols.1.so" target="_blank">libprot<wbr>ocols.1.so</a>(protocols::jd2::Fil<wbr>eSystemJobDistributor::go(std:<wbr>:shared_ptr<protocols::moves::<wbr>Mover>)+0x57) [0x7f3e344b4d67]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/bin/<wbr>erraser_minimizer.linuxgccrele<wbr>ase() [0x40480e]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/bin/<wbr>erraser_minimizer.linuxgccrele<wbr>ase() [0x4037b1]</div><div>/lib/x86_64-linux-gnu/libc.so.<wbr>6(__libc_start_main+0xf0) [0x7f3e32bdc830]</div><div>/home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/bin/<wbr>erraser_minimizer.linuxgccrele<wbr>ase() [0x4045b9]</div><div>Traceback (most recent call last):</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/build/../<wbr>modules/phenix/phenix/command_<wbr>line/erraser.py", line 14, in <module></div><div> erraser_run=phenix.erraser.err<wbr>aser.erraser(args=sys.argv[1:]<wbr>)</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>phenix/phenix/erraser/erraser.<wbr>py", line 349, in __init__</div><div> self.run(params,out=out)</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/modules/<wbr>phenix/phenix/erraser/erraser.<wbr>py", line 459, in run</div><div> erraser(option)</div><div> File "/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/src/<wbr>apps/public/ERRASER/erraser_<wbr>wrapper.py", line 99, in erraser</div><div> erraser_minimize( minimize_option ) #full_struct_slice_and_minimiz<wbr>e( minimize_option )</div><div> File "/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/src/<wbr>apps/public/ERRASER/erraser_<wbr>wrapper.py", line 478, in erraser_minimize</div><div> subprocess_call(command, sys.stdout, sys.stderr)</div><div> File "/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/src/<wbr>apps/public/ERRASER/erraser_<wbr>util.py", line 107, in subprocess_call</div><div> subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel)</div><div> File "/home/saibara/software/phenix<wbr>/phenix-dev-3092/base/lib/<wbr>python2.7/subprocess.py", line 186, in check_call</div><div> raise CalledProcessError(retcode, cmd)</div><div>subprocess.CalledProcessError: Command '/home/saibara/software/rosett<wbr>a/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/source/bin/<wbr>erraser_minimizer.linuxgccrele<wbr>ase -database /home/saibara/software/rosetta<wbr>/rosetta_bin_linux_2018.09.<wbr>60072_bundle/main/database/ -s /home/saibara/Phenix/hsmitorib<wbr>o_drug/rnaonly_erraser_temp/<wbr>minimize_0.pdb -score:weights stepwise/rna/rna_hires_elec_de<wbr>ns_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::erraser::rna_prot_errase<wbr>r 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_recor<wbr>ds true -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_m<wbr>ode true -use_2prime_OH_potential false -edensity:mapfile /home/saibara/Phenix/hsmitorib<wbr>o_drug/cheatmap.ccp4 -edensity:mapreso 3.0 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255</div></div><div><br></div></div>
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