Input: /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/domain0.fasta L : 91 Seq : TRCGCGTHAPSNCHARACTERIEDPRTEINSTHALASSISIRAPSEDNANAGNTHAPSDRAFTPESVMCMHVDLQVAMSSILSKLTGKDDT cp: `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/domain0.fasta' and `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/domain0.fasta' are the same file [[Executing: cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/domain0.fasta /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/]] DeepSF job id is domain0-2019-05-05-12-03-32 Process_ID : 155707581235157 Start_Time : Sun May 5 12:03:32 2019 Server_Name : DeepSF Job_Name : domain0 Email Id : File_Location : /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0.fasta Start_time : 1557075812 Command : perl /home/casp13/deepsf_3d//scripts/run_DeepSF-V1-2018-04-09.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/35157 /home/casp13/deepsf_3d//scripts/DeepSF_option Delay_Time : 0 Current_Time : 1557075812 perl /home/casp13/deepsf_3d//scripts/run_DeepSF-V1-2018-04-09.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/35157 /home/casp13/deepsf_3d//scripts/DeepSF_option mkdir: cannot create directory `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1': File exists ################## Start generating features for /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-seqs/DeepSF-domain0-155707581235157.feature_not_processed.fa ############# ################## Start open file /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-seqs/DeepSF-domain0-155707581235157.feature_not_processed.fa ############# Total number of sequences: 1 ########################### Start predicting SS and AA ############################# /home/casp13/DNCON2/SCRATCH-1D_1.1//bin/run_SCRATCH-1D_predictors.sh /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-seqs/DeepSF-domain0-155707581235157.feature_not_processed.fa /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH/DeepSF-domain0-155707581235157.feature_not_processed.fa 4 ################################### # # # SCRATCH-1D release 1.1 (2015) # # # ################################### [SCRATCH-1D_predictions.pl] 1 protein sequence(s) found [SCRATCH-1D_predictions.pl] generating sequence profiles... [SCRATCH-1D_predictions.pl] running SCRATCH-1D predictors... [SCRATCH-1D_predictions.pl] running homology analysis... [SCRATCH-1D_predictions.pl] writing SSpro predictions... [SCRATCH-1D_predictions.pl] writing SSpro8 predictions... [SCRATCH-1D_predictions.pl] writing ACCpro predictions... [SCRATCH-1D_predictions.pl] writing ACCpro20 predictions... [SCRATCH-1D_predictions.pl] job successfully completed! File /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH/DeepSF-domain0-155707581235157.feature_not_processed.fa.ss found File /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH/DeepSF-domain0-155707581235157.feature_not_processed.fa.acc found Start processing domain0 ########################### Start encoding SS ############################# perl /home/casp13/deepsf_3d//scripts/encoding_ss.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0.ss Starting encoding SS length 91 SS encoding finished ########################### Start encoding SA ############################# perl /home/casp13/deepsf_3d//scripts/encoding_acc.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0.acc Starting encoding SA length 91 SA encoding finished The sequence class is N The sequence is TRCGCGTHAPSNCHARACTERIEDPRTEINSTHALASSISIRAPSEDNANAGNTHAPSDRAFTPESVMCMHVDLQVAMSSILSKLTGKDDT The sequence length is 91 and the feature number is: 2275 ########################### Start encoding AA ############################# perl /home/casp13/deepsf_3d//scripts/gen_encoding.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0 Encoding Starting encoding AA AA encoding finished ########################### Start parsing results ############################# File /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0.aaencoding found File /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0.ss.ssencoding found File /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/SCRATCH//domain0/domain0.acc.saencoding found domain0 feature generated [blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix [blastpgp] WARNING: posReadCheckpoint: Attempting to recover data from previous checkpoint [blastpgp] WARNING: posReadCheckpoint: Data recovered successfully Creating feature folder: /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/PSSM/pssm_features/ Processing domain0 Processing /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features/PSSM The time started at : Sun May 5 12:44:44 2019. processing domain0.pssm python /home/casp13/deepsf_3d//scripts/DeepSF_predict.py /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-seqs/DeepSF-domain0-155707581235157.list_with_fea /home/casp13/deepsf_3d//scripts/database_SCOP/model_ResCNN_pssm-train-iterative-padding-withaa-complex-kmax30-win6_10_bias-sigmoid.json /home/casp13/deepsf_3d//scripts/database_SCOP/model_ResCNN_pssm-train-weight-iterative-padding-withaa-complex-kmax30-win6_10_bias-sigmoid_Te80.h5 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-predict-out/ 30 /home/casp13/deepsf_3d//scripts/database_SCOP/fold_label_relation2.txt Using Theano backend. /home/casp13/python_virtualenv/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters python /home/casp13/deepsf_3d//scripts/DeepSF_predict.py /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-seqs/DeepSF-domain0-155707581235157.list_with_fea /home/casp13/deepsf_3d//scripts/database_ECOD_X/model_ResCNN_pssm-train-iterative-padding-withaa-complex.json /home/casp13/deepsf_3d//scripts/database_ECOD_X/model_ResCNN_pssm-train-weight-iterative-padding-withaa-complex-best-val.h5 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-predict-out-ECOD_X/ 48 /home/casp13/deepsf_3d//scripts/database_ECOD_X/ecod.latest.fasta_id90_Xgroup_to_label_relation2.txt Using Theano backend. /home/casp13/python_virtualenv/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters python /home/casp13/deepsf_3d//scripts/DeepSF_predict.py /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-seqs/DeepSF-domain0-155707581235157.list_with_fea /home/casp13/deepsf_3d//scripts/database_ECOD_H/model_ResCNN_pssm-train-iterative-padding-withaa-complex.json /home/casp13/deepsf_3d//scripts/database_ECOD_H/model_ResCNN_pssm-train-weight-iterative-padding-withaa-complex-best-val.h5 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-features /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-predict-out-ECOD_H/ 46 /home/casp13/deepsf_3d//scripts/database_ECOD_H/ecod.latest.fasta_id90_XHgroup_to_label_relation2.txt Using Theano backend. /home/casp13/python_virtualenv/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. from ._conv import register_converters as _register_converters Processing domain0 Predict 1:domain0 Waiting /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-KL-hidden-out/score_ranking_dir/domain0_KL_calc.done Waiting /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-KL-hidden-out/score_ranking_dir/domain0_template_fea.txt.done Processing domain0 Predict 1:domain0 Waiting /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-KL-hidden-out-ECOD_X/score_ranking_dir/domain0_KL_calc.done Waiting /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-KL-hidden-out-ECOD_X/score_ranking_dir/domain0_template_fea.txt.done Processing domain0 Predict 1:domain0 Waiting /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-KL-hidden-out-ECOD_H/score_ranking_dir/domain0_KL_calc.done Waiting /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-KL-hidden-out-ECOD_H/score_ranking_dir/domain0_template_fea.txt.done Generate hhm: perl /home/casp13/deepsf_3d//scripts/generate_hhm.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/seqs//domain0.fasta /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/ domain0 /home/casp13/deepsf_3d/ /home/casp13/deepsf_3d/deepsf3d_tools/hhsuite-2.0.16-linux-x86_64/ Name "main::template_file" used only once: possible typo at /home/casp13/deepsf_3d//scripts/generate_hhm.pl line 60. generate .a3m in HHsearchHits perl /home/casp13/deepsf_3d//scripts/hhsearch_scripts/buildali15.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm//domain0.fasta >> /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm//HHsearchHits.log 2>&1 generate .hhm in HHsearchHits /home/casp13/deepsf_3d/deepsf3d_tools/hhsuite-2.0.16-linux-x86_64//bin//hhmake -i /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm//domain0.a3m &> /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm//HHsearchHits.log perl /home/casp13/deepsf_3d//scripts/generate_alignment_by_hhalign.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/ /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/ /home/casp13/deepsf_3d/ /home/casp13/deepsf_3d/deepsf3d_tools/hhsuite-2.0.16-linux-x86_64/ perl /home/casp13/deepsf_3d//scripts/generate_alignment_by_prosmal3d.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/ /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/ /home/casp13/deepsf_3d/ /home/casp13/deepsf_3d/deepsf3d_tools/promals_structure_MSA/ /home/casp13/deepsf_3d/deepsf3d_tools/promals_package/ The process id of the thread 1 is 36307. The process id of the thread 2 is 36308. The process id of the thread 3 is 36309. The process id of the thread 4 is 36310. The process id of the thread 5 is 36311. start thread 5 #### Running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info on batch 5 start thread 1 #### Running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info on batch 1 start thread 4 #### Running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info on batch 4 start thread 3 #### Running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info on batch 3 start thread 2 #### Running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info on batch 2 ####################### Summarize the SCOP alignment #### Generating alignment between SCOP_fold_f.23_top10 by promal3d #### Generating alignment between SCOP_fold_a.60_top10 by promal3d #### Generating alignment between SCOP_fold_g.39_top10 by promal3d #### Generating alignment between SCOP_fold_c.15_top10 by promal3d #### Generating alignment between SCOP_fold_g.50_top10 by promal3d ####################### Summarize the ECOD-X alignment #### Generating alignment between ECOD_X_fold_X.5040_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.6070_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.244_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.330_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.12_top10 by promal3d ####################### Summarize the ECOD-H alignment #### Generating alignment between ECOD_H_fold_X.378.1_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.3481.1_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.304.35_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.3216.1_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.2.1_top10 by promal3d Running hhsearch151 on templates perl /home/casp13/deepsf_3d//scripts/generate_alignment_by_hhsearch151.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0.fasta /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/ /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/ /home/casp13/deepsf_3d/ /home/casp13/deepsf_3d/deepsf3d_tools/hhsearch1.5.1/ Name "main::prosys_dir" used only once: possible typo at /home/casp13/deepsf_3d//scripts/hhsearch_scripts/local2model_simple.pl line 117. Running hmmer3 on templates perl /home/casp13/deepsf_3d//scripts/generate_alignment_by_jackhammer.pl /home/casp13/deepsf_3d//scripts/hhsearch_scripts/jackhammer_option /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0.fasta /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/ /home/casp13/deepsf_3d/ /home/casp13/deepsf_3d/deepsf3d_tools/hmmer-3.1b2-linux-intel-x86_64/binaries/ No templates with evalue than 1 were found. Stop! 0rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/domain0/hhalign/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/domain0/hhalign/*/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/domain0/promal3d/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/domain0/promal3d/*/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/*/bak_*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/*/*B99990001*pdb': No such file or directory cp: cannot stat `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/*/*pdb': No such file or directory cp: cannot stat `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/domain0/jackhammer/*pdb': No such file or directory cp: cannot stat `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-alignment/domain0/jackhammer/*pir': No such file or directory cp: cannot stat `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/webserver_packages': No such file or directory perl /home/casp13/deepsf_3d//scripts/gen_consensus_aln.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/Domain_Check/ domain0 /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/domain0.fasta /home/casp13/deepsf_3d// ************************************************** run alignment_check.pl ########### Start refine domain0_e1e6vC1 The initial coverage for domain0_e1e6vC1 is 0.263736263736264 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e1e6vC1 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e5a8rL1 The initial coverage for domain0_e5a8rL1 is 0.263736263736264 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e5a8rL1 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_d5gata__glob The initial coverage for domain0_d5gata__glob is 0.483516483516484 Iteration 1 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_d5gata__glob is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_d2c7na1_glob The initial coverage for domain0_d2c7na1_glob is 0.274725274725275 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_d2c7na1_glob is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e5kvhA3_glob The initial coverage for domain0_e5kvhA3_glob is 0.208791208791209 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e5kvhA3_glob is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_d1l7ba__glob The initial coverage for domain0_d1l7ba__glob is 0.21978021978022 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_d1l7ba__glob is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e4po7A1_glob The initial coverage for domain0_e4po7A1_glob is 0.241758241758242 Iteration 1 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e4po7A1_glob is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e2rsmA1 The initial coverage for domain0_e2rsmA1 is 0.725274725274725 Iteration 1 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e2rsmA1 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e1e6yC1 The initial coverage for domain0_e1e6yC1 is 0.252747252747253 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e1e6yC1 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e1qu6A1 The initial coverage for domain0_e1qu6A1 is 0.32967032967033 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e1qu6A1 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e3cihA3 The initial coverage for domain0_e3cihA3 is 0.230769230769231 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e3cihA3 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain0_e3sqgC1 The initial coverage for domain0_e3sqgC1 is 0.263736263736264 Iteration 1 finished! Improving coverage to 0.725274725274725 Iteration 2 finished! Improving coverage to 0.791208791208791 Coverage converged!Quit.... The final coverage for domain0_e3sqgC1 is: 0.791208791208791 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### Fasta length: 91 Checking if existing hard region Starting generating models under [[Executing: cp ./ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh ./ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./SCOP_fold_c.15_top10_for_modeling_pir_dir.sh ./SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./CONSENSUS_for_modeling_pir_dir.sh ./CONSENSUS_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./SCOP_fold_g.39_top10_for_modeling_pir_dir.sh ./SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.queued]] Current queue seqs counts for 3D modeling: 8 Current running seqs counts for 3D modeling: 0 [Sun May 5 14:48:37 2019] Starting CONSENSUS_for_modeling_pir_dir.sh Executing ./CONSENSUS_for_modeling_pir_dir.sh &> ./CONSENSUS_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 8 Current running seqs counts for 3D modeling: 0 [Sun May 5 14:48:37 2019] Starting ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh Executing ./ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh &> ./ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 6 Current running seqs counts for 3D modeling: 2 [Sun May 5 14:48:44 2019] Starting ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.12_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 5 Current running seqs counts for 3D modeling: 3 [Sun May 5 14:48:49 2019] Starting SCOP_fold_c.15_top10_for_modeling_pir_dir.sh Executing ./SCOP_fold_c.15_top10_for_modeling_pir_dir.sh &> ./SCOP_fold_c.15_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 4 Current running seqs counts for 3D modeling: 4 [Sun May 5 14:48:54 2019] Starting ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 3 Current running seqs counts for 3D modeling: 5 [Sun May 5 14:48:59 2019] Starting ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.244_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue modeling job counts for 3D modeling: 2 Current running modeling job counts for 3D modeling: 6 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.12_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue seqs counts for 3D modeling: 2 Current running seqs counts for 3D modeling: 5 [Sun May 5 14:49:04 2019] Starting ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.330_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue modeling job counts for 3D modeling: 1 Current running modeling job counts for 3D modeling: 6 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_c.15_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue seqs counts for 3D modeling: 1 Current running seqs counts for 3D modeling: 5 [Sun May 5 14:49:09 2019] Starting SCOP_fold_g.39_top10_for_modeling_pir_dir.sh Executing ./SCOP_fold_g.39_top10_for_modeling_pir_dir.sh &> ./SCOP_fold_g.39_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue modeling job counts for 3D modeling: 0 Current running modeling job counts for 3D modeling: 6 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.6070_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue modeling job counts for 3D modeling: 0 Current running modeling job counts for 3D modeling: 5 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.244_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue modeling job counts for 3D modeling: 0 Current running modeling job counts for 3D modeling: 4 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_H_fold_X.304.35_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue modeling job counts for 3D modeling: 0 Current running modeling job counts for 3D modeling: 3 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/SCOP_fold_g.39_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue modeling job counts for 3D modeling: 0 Current running modeling job counts for 3D modeling: 2 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/ECOD_X_fold_X.330_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue modeling job counts for 3D modeling: 0 Current running modeling job counts for 3D modeling: 1 Found /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/CONSENSUS_for_modeling_pir_dir.sh.cameo.done]] All 3D modeling are running, move to next job Start Evaluation rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/*/bak_*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0-hhm/domain0/*/*B99990001*pdb': No such file or directory generating SBROD score ./assess_protein /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models_convert/* &> /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/output/SBROD_ranking.txt SBROD modeling finished within 0.104444444444444 hrs! Checking /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/output/SBROD_ranking.txt ###################### Start to format the top 5 models, rename the target id to CAMEO id Total lines: 36 in /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/output/Final_ranking.txt ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models//domain0_e4po7A1_glob_consensus.pdb /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/temp//casp1.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/alignments//domain0_e4po7A1_glob_consensus.pir /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5_aln//casp1.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models//domain0_e2rsmA1.pdb /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/temp//casp2.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/alignments//domain0_e2rsmA1.pir /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5_aln//casp2.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models//hg2.pdb /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/temp//casp3.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/alignments//hg2.pir /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5_aln//casp3.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models//hg4.pdb /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/temp//casp4.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/alignments//hg4.pir /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5_aln//casp4.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models//domain0_d2c7na1_glob.pdb /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/temp//casp5.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/alignments//domain0_d2c7na1_glob.pir /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5_aln//casp5.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/models//ECOD_X_fold_X.330_top10_for_modeling_hhalign.pdb /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/temp//casp6.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/EVALUATION/alignments//ECOD_X_fold_X.330_top10_for_modeling_hhalign.pir /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5_aln//casp6.pir perl /home/casp13/deepsf_3d//scripts/formatCAMEOmodel.pl /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/deepsf_stage1/domain0.fasta domain0 /home/casp13/deepsf_3d/ &>> /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/formatCASPmodel.log Start to refine models to top 5 models DeepSF-3D modeling finish! Total time: <2.89666666666667> hrs! Finished [/home/casp13/deepsf_3d/scripts/deepsf-main-V1-2018-04-09.pl]: Sun May 5 14:57:20 2019, models are saving in /home/casp11/multicom/ZCA_155705426023607/domain0/deepsf/TOP5/