Branch: rosetta:commits 「revision: №20464」
Test: linux.clang.integration.release_debug_no_symbols
SubTest: identify_cdr_clusters
SubTest files: 「file-system-view」
Daemon: hojo-4    
State: identify_cdr_clusters

Brief Diff: Only in /home/benchmark/working_dir/main:62124/identify_cdr_clusters: 2j88_renum_0001.pdb Files /home/benchmark/working_dir/main:62124/identify_cdr_clusters/log and /home/benchmark/working_dir/commits:20464/identify_cdr_clusters/log differ Only in /home/benchmark/working_dir/commits:20464/identify_cdr_clusters: ROSETTA_CRASH.log Only in /home/benchmark/working_dir/main:62124/identify_cdr_clusters: score.sc Only in /home/benchmark/working_dir/commits:20464/identify_cdr_clusters: .test_did_not_run.log Full Diff: Only in /home/benchmark/working_dir/main:62124/identify_cdr_clusters: 2j88_renum_0001.pdb diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62124/identify_cdr_clusters/log /home/benchmark/working_dir/commits:20464/identify_cdr_clusters/log 393,475c393 < basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt < protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully < protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully < antibody.AntibodyInfo: Successfully finished the CDR definition < antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type < antibody.AntibodyInfo: TLYYGSVDYW < antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: EXTENDED < antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 0 Extended: 1 < antibody.AntibodyInfo: Setting up CDR Cluster for H1 < protocols.antibody.cluster.CDRClusterMatcher: Length: 15 Omega: TTTTTTTTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for H2 < protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for H3 < protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for L1 < protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for L2 < protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for L3 < protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT < //////////////////////////////////////////////////////////////////////////////// < /// Rosetta Antibody Info /// < /// /// < /// Antibody Type: Regular Antibody < /// Light Chain Type: unknown < /// Predict H3 Cterminus Base: EXTENDED < /// < /// H1 info: < /// length: 15 < /// sequence: SFSGFSLSTSGMGVS < /// north_cluster: H1-15-1 < /// loop_info: LOOP start: 513 stop: 527 cut: 520 size: 15 skip rate: 0 extended?: False < < /// H2 info: < /// length: 9 < /// sequence: HIYWDDDKR < /// north_cluster: H2-9-1 < /// loop_info: LOOP start: 542 stop: 550 cut: 546 size: 9 skip rate: 0 extended?: False < < /// H3 info: < /// length: 9 < /// sequence: TLYYGSVDY < /// north_cluster: H3-9-1 < /// loop_info: LOOP start: 588 stop: 596 cut: 589 size: 9 skip rate: 0 extended?: False < < /// L1 info: < /// length: 11 < /// sequence: RASENIYSYLT < /// north_cluster: L1-11-1 < /// loop_info: LOOP start: 343 stop: 353 cut: 348 size: 11 skip rate: 0 extended?: False < < /// L2 info: < /// length: 8 < /// sequence: YNAKTLAE < /// north_cluster: L2-8-1 < /// loop_info: LOOP start: 367 stop: 374 cut: 371 size: 8 skip rate: 0 extended?: False < < /// L3 info: < /// length: 8 < /// sequence: QHHYGTRT < /// north_cluster: L3-8-1 < /// loop_info: LOOP start: 407 stop: 414 cut: 411 size: 8 skip rate: 0 extended?: False < < //////////////////////////////////////////////////////////////////////////////// < antibody.AntibodyInfo: Setting up CDR Cluster for H1 < protocols.antibody.cluster.CDRClusterMatcher: Length: 15 Omega: TTTTTTTTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for H2 < protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for H3 < protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for L1 < protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for L2 < protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT < antibody.AntibodyInfo: Setting up CDR Cluster for L3 < protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT < < REMARK CLUSTER H1-15-1 16.1346 < REMARK CLUSTER H2-9-1 14.4206 < REMARK CLUSTER H3-9-1 40.5791 < REMARK CLUSTER L1-11-1 14.8194 < REMARK CLUSTER L2-8-1 9.02117 < REMARK CLUSTER L3-8-1 49.5321 --- > protocols.jd2.JobDistributor: [ ERROR ] 477c395 < Info added to any echo PDB --- > [ERROR] Exception caught by JobDistributor for job 2j88_renum_0001 479c397,416 < protocols.jd2.JobDistributor: no more batches to process... --- > [ ERROR ]: Caught exception: > > > File: src/core/pose/chains_util.cc:455 > chain_id L represents more than one chain! > ------------------------ Begin developer's backtrace ------------------------- > BACKTRACE: > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libutility.so(backtrace_string(int)+0x34) [0x7fdce854dca4] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x55) [0x7fdce8579055] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libcore.3.so(core::pose::get_chain_id_from_chain(char const&, core::pose::Pose const&)+0x2ba) [0x7fdceaeb83da] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libprotocols.7.so(protocols::antibody::AntibodyInfo::identify_antibody(core::pose::Pose const&)+0xa4) [0x7fdcf717f114] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libprotocols.7.so(protocols::antibody::AntibodyInfo::AntibodyInfo(core::pose::Pose const&, protocols::antibody::CDRDefinitionEnum, bool)+0x4b3) [0x7fdcf7181103] > ROSETTA/source/bin/identify_cdr_clusters.default.linuxclangrelease_debug_no_symbols() [0x40419b] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x2378) [0x7fdcee6e4f78] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x11f) [0x7fdcee6e194f] > ROSETTA/source/build/src/release_debug_no_symbols/linux/5.4/64/x86/clang/3.4/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x64) [0x7fdcee6db814] > ROSETTA/source/bin/identify_cdr_clusters.default.linuxclangrelease_debug_no_symbols() [0x4035dd] > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fdce5427555] > ROSETTA/source/bin/identify_cdr_clusters.default.linuxclangrelease_debug_no_symbols() [0x4034b9] > ------------------------- End developer's backtrace -------------------------- 482c419 < App Author: Jared Adolf-Bryfogle; PI: Roland Dunbrack --- > AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. 484d420 < CDR Classification done using the same methodology as PyIgClassify. 486,488c422,429 < Please cite RosettaAntibody and the following: < Adolf-Bryfogle J, Xu Q, North B, Lehmann A, Dunbrack RL. PyIgClassify: a database of antibody CDR structural classifications. Nucleic Acids Res 2015; 43:D432-D438. < North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011; 406:228-256. --- > protocols.jd2.JobDistributor: [ WARNING ] 2j88_renum_0001 reported failure and will NOT retry > protocols.jd2.JobDistributor: no more batches to process... > > --------------------------------------------------------------- > [ ERROR ]: Error(s) were encountered when running jobs. > 1 jobs failed; > Check the output further up for additional error messages. > --------------------------------------------------------------- Only in /home/benchmark/working_dir/commits:20464/identify_cdr_clusters: ROSETTA_CRASH.log Only in /home/benchmark/working_dir/main:62124/identify_cdr_clusters: score.sc Only in /home/benchmark/working_dir/commits:20464/identify_cdr_clusters: .test_did_not_run.log Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!