Input: /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/domain1.fasta L : 218 Seq : GKDDTSAPPLTPKDIVAALQSRGWEAEIISASSISQDMVEVDPAGILKCVDGRGSDNTRMAGPKMPGGIYAIAHNRGTTSVDGLKEITKEVASKGHVPSVHGDHSADMLGCGFFRLWVTGEFDSMGYPRPEFDADQGAAAVKESGGVIEMHHGSHTEKVVYINLVENKTLEPDENDQRFIVDGWAAIKFNLDVVKFLVAAAATVEMLGGPRIAKIVVA cp: `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/domain1.fasta' and `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/domain1.fasta' are the same file [[Executing: cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/domain1.fasta /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/]] DeepSF job id is domain1-2019-05-05-20-20-26 Process_ID : 155710562725400 Start_Time : Sun May 5 20:20:27 2019 Server_Name : DeepSF Job_Name : domain1 Email Id : File_Location : /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1.fasta Start_time : 1557105627 Command : perl /home/casp13/deepsf_3d//scripts/run_DeepSF-V1-2018-04-09.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/25400 /home/casp13/deepsf_3d//scripts/DeepSF_option Delay_Time : 0 Current_Time : 1557105627 perl /home/casp13/deepsf_3d//scripts/run_DeepSF-V1-2018-04-09.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/25400 /home/casp13/deepsf_3d//scripts/DeepSF_option mkdir: cannot create directory `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1': File exists ################## Start generating features for /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-seqs/DeepSF-domain1-155710562725400.feature_not_processed.fa ############# ################## Start open file /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-seqs/DeepSF-domain1-155710562725400.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/domain1/deepsf/deepsf_stage1/domain1-seqs/DeepSF-domain1-155710562725400.feature_not_processed.fa /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH/DeepSF-domain1-155710562725400.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/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH/DeepSF-domain1-155710562725400.feature_not_processed.fa.ss found File /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH/DeepSF-domain1-155710562725400.feature_not_processed.fa.acc found Start processing domain1 ########################### Start encoding SS ############################# perl /home/casp13/deepsf_3d//scripts/encoding_ss.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1 /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1.ss Starting encoding SS length 218 SS encoding finished ########################### Start encoding SA ############################# perl /home/casp13/deepsf_3d//scripts/encoding_acc.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1 /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1.acc Starting encoding SA length 218 SA encoding finished The sequence class is N The sequence is GKDDTSAPPLTPKDIVAALQSRGWEAEIISASSISQDMVEVDPAGILKCVDGRGSDNTRMAGPKMPGGIYAIAHNRGTTSVDGLKEITKEVASKGHVPSVHGDHSADMLGCGFFRLWVTGEFDSMGYPRPEFDADQGAAAVKESGGVIEMHHGSHTEKVVYINLVENKTLEPDENDQRFIVDGWAAIKFNLDVVKFLVAAAATVEMLGGPRIAKIVVA The sequence length is 218 and the feature number is: 5450 ########################### Start encoding AA ############################# perl /home/casp13/deepsf_3d//scripts/gen_encoding.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1 /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1 Encoding Starting encoding AA AA encoding finished ########################### Start parsing results ############################# File /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1.aaencoding found File /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1.ss.ssencoding found File /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/SCRATCH//domain1/domain1.acc.saencoding found domain1 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/domain1/deepsf/deepsf_stage1/domain1-features/PSSM/pssm_features/ Processing domain1 Processing /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features/PSSM The time started at : Sun May 5 21:09:26 2019. processing domain1.pssm python /home/casp13/deepsf_3d//scripts/DeepSF_predict.py /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-seqs/DeepSF-domain1-155710562725400.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/domain1/deepsf/deepsf_stage1/domain1-features /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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/domain1/deepsf/deepsf_stage1/domain1-seqs/DeepSF-domain1-155710562725400.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/domain1/deepsf/deepsf_stage1/domain1-features /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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/domain1/deepsf/deepsf_stage1/domain1-seqs/DeepSF-domain1-155710562725400.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/domain1/deepsf/deepsf_stage1/domain1-features /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-features /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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 domain1 Predict 1:domain1 Waiting /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-KL-hidden-out/score_ranking_dir/domain1_KL_calc.done Waiting /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-KL-hidden-out/score_ranking_dir/domain1_template_fea.txt.done Processing domain1 Predict 1:domain1 Waiting /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-KL-hidden-out-ECOD_X/score_ranking_dir/domain1_KL_calc.done Waiting /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-KL-hidden-out-ECOD_X/score_ranking_dir/domain1_template_fea.txt.done Processing domain1 Predict 1:domain1 Waiting /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-KL-hidden-out-ECOD_H/score_ranking_dir/domain1_KL_calc.done Waiting /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-KL-hidden-out-ECOD_H/score_ranking_dir/domain1_template_fea.txt.done Generate hhm: perl /home/casp13/deepsf_3d//scripts/generate_hhm.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/seqs//domain1.fasta /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/ domain1 /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/domain1/deepsf/deepsf_stage1/domain1-hhm//domain1.fasta >> /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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/domain1/deepsf/deepsf_stage1/domain1-hhm//domain1.a3m &> /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm//HHsearchHits.log perl /home/casp13/deepsf_3d//scripts/generate_alignment_by_hhalign.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/ /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/ /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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 712. start thread 1 #### Running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info on batch 1 The process id of the thread 2 is 713. start thread 2 #### Running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info on batch 2 The process id of the thread 3 is 715. start thread 3 #### Running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info on batch 3 The process id of the thread 4 is 717. start thread 4 #### Running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info on batch 4 The process id of the thread 5 is 719. start thread 5 #### Running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info on batch 5 ####################### Summarize the SCOP alignment #### Generating alignment between SCOP_fold_c.154_top10 by promal3d #### Generating alignment between SCOP_fold_c.66_top10 by promal3d #### Generating alignment between SCOP_fold_c.94_top10 by promal3d #### Generating alignment between SCOP_fold_d.145_top10 by promal3d #### Generating alignment between SCOP_fold_a.4_top10 by promal3d ####################### Summarize the ECOD-X alignment #### Generating alignment between ECOD_X_fold_X.2002_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.2007_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.2111_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.219_top10 by promal3d #### Generating alignment between ECOD_X_fold_X.2003_top10 by promal3d ####################### Summarize the ECOD-H alignment #### Generating alignment between ECOD_H_fold_X.2002.1_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.4126.2_top10 by promal3d Failed to find /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/domain1/hhalign/domain1_e4u7tB1.pir #### Generating alignment between ECOD_H_fold_X.2003.1_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.314.1_top10 by promal3d #### Generating alignment between ECOD_H_fold_X.2011.1_top10 by promal3d Running hhsearch151 on templates perl /home/casp13/deepsf_3d//scripts/generate_alignment_by_hhsearch151.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1.fasta /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/ /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-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/domain1/deepsf/deepsf_stage1/domain1.fasta /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/query_template_list.info /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/ /home/casp13/deepsf_3d/ /home/casp13/deepsf_3d/deepsf3d_tools/hmmer-3.1b2-linux-intel-x86_64/binaries/ Name "main::prosys_dir" used only once: possible typo at /home/casp13/deepsf_3d//scripts/hhsearch_scripts/local2model_simple.pl line 117. 0rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/domain1/hhalign/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/domain1/hhalign/*/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/domain1/promal3d/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-alignment/domain1/promal3d/*/*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/*/bak_*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/*/*B99990001*pdb': No such file or directory cp: cannot stat `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/*/*pdb': No such file or directory cp: cannot stat `/home/casp11/multicom/ZCA_155705426023607/domain1/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/domain1/deepsf/Domain_Check/ domain1 /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/domain1.fasta /home/casp13/deepsf_3d// ************************************************** run alignment_check.pl ########### Start refine domain1_e2p10A1 The initial coverage for domain1_e2p10A1 is 0.270642201834862 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e2p10A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1riqA2 The initial coverage for domain1_e1riqA2 is 0.23394495412844 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1riqA2 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_d3boja1 The initial coverage for domain1_d3boja1 is 0.894495412844037 Iteration 1 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_d3boja1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3r8rA1_glob The initial coverage for domain1_e3r8rA1_glob is 0.307339449541284 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3r8rA1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e2qvpC1_glob The initial coverage for domain1_e2qvpC1_glob is 0.243119266055046 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e2qvpC1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e4u7tB1 The initial coverage for domain1_e4u7tB1 is 0.23394495412844 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e4u7tB1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3bohB1 The initial coverage for domain1_e3bohB1 is 0.894495412844037 Iteration 1 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3bohB1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3boeA1 The initial coverage for domain1_e3boeA1 is 0.954128440366973 Iteration 1 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3boeA1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1yx1A1 The initial coverage for domain1_e1yx1A1 is 0.55045871559633 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1yx1A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e2htmA1_glob The initial coverage for domain1_e2htmA1_glob is 0.321100917431193 Iteration 1 finished! Improving coverage to 0.977064220183486 Iteration 2 finished! Improving coverage to 1 Coverage converged!Quit.... The final coverage for domain1_e2htmA1_glob is: 1 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3s46A1 The initial coverage for domain1_e3s46A1 is 0.229357798165138 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3s46A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_d2ezha__glob The initial coverage for domain1_d2ezha__glob is 0.211009174311927 Iteration 1 finished! Improving coverage to 0.977064220183486 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_d2ezha__glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3shoA1_glob The initial coverage for domain1_e3shoA1_glob is 0.422018348623853 Iteration 1 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3shoA1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3uk8A1 The initial coverage for domain1_e3uk8A1 is 0.972477064220184 Iteration 1 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3uk8A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_d3boea1 The initial coverage for domain1_d3boea1 is 0.954128440366973 Iteration 1 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_d3boea1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3dsqB1_glob The initial coverage for domain1_e3dsqB1_glob is 0.399082568807339 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3dsqB1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_d2p4pa1_glob The initial coverage for domain1_d2p4pa1_glob is 0.211009174311927 Iteration 1 finished! Improving coverage to 0.977064220183486 Iteration 2 finished! Improving coverage to 1 Coverage converged!Quit.... The final coverage for domain1_d2p4pa1_glob is: 1 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e4wckA1_glob The initial coverage for domain1_e4wckA1_glob is 0.188073394495413 Iteration 1 finished! Improving coverage to 0.977064220183486 Iteration 2 finished! Improving coverage to 1 Coverage converged!Quit.... The final coverage for domain1_e4wckA1_glob is: 1 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_d1nh8a1_glob The initial coverage for domain1_d1nh8a1_glob is 0.311926605504587 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_d1nh8a1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e4xeoB1 The initial coverage for domain1_e4xeoB1 is 0.408256880733945 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e4xeoB1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1lqjC1 The initial coverage for domain1_e1lqjC1 is 0.394495412844037 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1lqjC1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e2z84A1 The initial coverage for domain1_e2z84A1 is 0.188073394495413 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e2z84A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e5an7A1 The initial coverage for domain1_e5an7A1 is 0.201834862385321 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e5an7A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3vabA2 The initial coverage for domain1_e3vabA2 is 0.348623853211009 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3vabA2 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1kmnB1 The initial coverage for domain1_e1kmnB1 is 0.330275229357798 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1kmnB1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e5crbA1 The initial coverage for domain1_e5crbA1 is 0.490825688073394 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e5crbA1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3tr7A1 The initial coverage for domain1_e3tr7A1 is 0.399082568807339 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3tr7A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1ww8A1 The initial coverage for domain1_e1ww8A1 is 0.321100917431193 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1ww8A1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e3pbiA1 The initial coverage for domain1_e3pbiA1 is 0.201834862385321 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e3pbiA1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e5hzyA1 The initial coverage for domain1_e5hzyA1 is 0.380733944954128 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e5hzyA1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1twiA2 The initial coverage for domain1_e1twiA2 is 0.362385321100917 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1twiA2 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e1l6wA1_glob The initial coverage for domain1_e1l6wA1_glob is 0.339449541284404 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e1l6wA1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e2cvzA2 The initial coverage for domain1_e2cvzA2 is 0.23394495412844 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e2cvzA2 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_d1z7me1_glob The initial coverage for domain1_d1z7me1_glob is 0.31651376146789 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_d1z7me1_glob is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### ########### Start refine domain1_e2jhqA1 The initial coverage for domain1_e2jhqA1 is 0.403669724770642 Iteration 1 finished! Improving coverage to 0.972477064220184 Iteration 2 finished! Improving coverage to 0.995412844036697 Coverage converged!Quit.... The final coverage for domain1_e2jhqA1 is: 0.995412844036697 ##### Search hard region among alignment coverage using neighborhood pairwise examination ##### Fasta length: 218 Checking if existing hard region Starting generating models under [[Executing: cp ./SCOP_fold_c.94_top10_for_modeling_pir_dir.sh ./SCOP_fold_c.94_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh ./ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh ./ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./SCOP_fold_c.154_top10_for_modeling_pir_dir.sh ./SCOP_fold_c.154_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./SCOP_fold_a.4_top10_for_modeling_pir_dir.sh ./SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh ./ECOD_H_fold_X.2002.1_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_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh ./ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh ./ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh.cameo.queued]] [[Executing: cp ./SCOP_fold_d.145_top10_for_modeling_pir_dir.sh ./SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.queued]] Current queue seqs counts for 3D modeling: 14 Current running seqs counts for 3D modeling: 0 [Sun May 5 23:47:10 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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/CONSENSUS_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/CONSENSUS_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 14 Current running seqs counts for 3D modeling: 0 [Sun May 5 23:47:10 2019] Starting ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 12 Current running seqs counts for 3D modeling: 2 [Sun May 5 23:47:15 2019] Starting ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 11 Current running seqs counts for 3D modeling: 3 [Sun May 5 23:47:20 2019] Starting SCOP_fold_c.154_top10_for_modeling_pir_dir.sh Executing ./SCOP_fold_c.154_top10_for_modeling_pir_dir.sh &> ./SCOP_fold_c.154_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 10 Current running seqs counts for 3D modeling: 4 [Sun May 5 23:47:25 2019] Starting ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh Executing ./ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh &> ./ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 9 Current running seqs counts for 3D modeling: 5 [Sun May 5 23:47:30 2019] Starting ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.219_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 8 Current running seqs counts for 3D modeling: 6 [Sun May 5 23:47:35 2019] Starting ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh Executing ./ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh &> ./ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 7 Current running seqs counts for 3D modeling: 7 [Sun May 5 23:47:40 2019] Starting SCOP_fold_a.4_top10_for_modeling_pir_dir.sh Executing ./SCOP_fold_a.4_top10_for_modeling_pir_dir.sh &> ./SCOP_fold_a.4_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue modeling job counts for 3D modeling: 6 Current running modeling job counts for 3D modeling: 8 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2003_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue seqs counts for 3D modeling: 6 Current running seqs counts for 3D modeling: 7 [Sun May 5 23:47:45 2019] Starting SCOP_fold_d.145_top10_for_modeling_pir_dir.sh Executing ./SCOP_fold_d.145_top10_for_modeling_pir_dir.sh &> ./SCOP_fold_d.145_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 5 Current running seqs counts for 3D modeling: 8 [Sun May 5 23:47:50 2019] Starting ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh Executing ./ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh &> ./ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue seqs counts for 3D modeling: 4 Current running seqs counts for 3D modeling: 9 [Sun May 5 23:47:55 2019] Starting ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh Executing ./ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh &> ./ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh.cameo.running]] Current queue modeling job counts for 3D modeling: 3 Current running modeling job counts for 3D modeling: 10 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2111_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue modeling job counts for 3D modeling: 3 Current running modeling job counts for 3D modeling: 9 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2011.1_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue seqs counts for 3D modeling: 3 Current running seqs counts for 3D modeling: 8 [Sun May 5 23:48:00 2019] Starting SCOP_fold_c.94_top10_for_modeling_pir_dir.sh Executing ./SCOP_fold_c.94_top10_for_modeling_pir_dir.sh &> ./SCOP_fold_c.94_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_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: 9 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_a.4_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue seqs counts for 3D modeling: 2 Current running seqs counts for 3D modeling: 8 [Sun May 5 23:48:05 2019] Starting ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_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: 9 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_d.145_top10_for_modeling_pir_dir.sh.cameo.done]] Current queue seqs counts for 3D modeling: 1 Current running seqs counts for 3D modeling: 8 [Sun May 5 23:48:10 2019] Starting ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh Executing ./ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh &> ./ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.log & [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh.cameo.queued /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_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: 9 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.2002.1_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: 8 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.154_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: 7 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.219_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: 6 Found /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/SCOP_fold_c.94_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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2007_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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.314.1_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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_H_fold_X.4126.2_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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_top10_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/ECOD_X_fold_X.2002_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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/CONSENSUS_for_modeling_pir_dir.modeling.done mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/CONSENSUS_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/CONSENSUS_for_modeling_pir_dir.sh.cameo.done [[Executing: mv /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/CONSENSUS_for_modeling_pir_dir.sh.cameo.running /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/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/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/*/bak_*pdb': No such file or directory rm: cannot remove `/home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1-hhm/domain1/*/*B99990001*pdb': No such file or directory generating SBROD score ./assess_protein /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models_convert/* &> /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/output/SBROD_ranking.txt SBROD modeling finished within 0.0480555555555556 hrs! Checking /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/output/SBROD_ranking.txt ###################### Start to format the top 5 models, rename the target id to CAMEO id Total lines: 93 in /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/output/Final_ranking.txt ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models//domain1_d3boea1.pdb /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/temp//casp1.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/alignments//domain1_d3boea1.pir /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5_aln//casp1.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models//domain1_e3boeA1.pdb /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/temp//casp2.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/alignments//domain1_e3boeA1.pir /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5_aln//casp2.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models//hg3.pdb /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/temp//casp3.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/alignments//hg3.pir /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5_aln//casp3.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models//SCOP_fold_c.154_top10_for_modeling_hhalign.pdb /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/temp//casp4.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/alignments//SCOP_fold_c.154_top10_for_modeling_hhalign.pir /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5_aln//casp4.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models//hg2.pdb /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/temp//casp5.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/alignments//hg2.pir /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5_aln//casp5.pir ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/models//hg1.pdb /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/temp//casp6.pdb ### cp /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/EVALUATION/alignments//hg1.pir /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5_aln//casp6.pir perl /home/casp13/deepsf_3d//scripts/formatCAMEOmodel.pl /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/deepsf_stage1/domain1.fasta domain1 /home/casp13/deepsf_3d/ &>> /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/formatCASPmodel.log Start to refine models to top 5 models DeepSF-3D modeling finish! Total time: <3.72166666666667> hrs! Finished [/home/casp13/deepsf_3d/scripts/deepsf-main-V1-2018-04-09.pl]: Mon May 6 00:03:44 2019, models are saving in /home/casp11/multicom/ZCA_155705426023607/domain1/deepsf/TOP5/