echo remote 2track remote 2track make -k PRED=1dl2A PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make -k \ 1dl2A/T0120-116-210-1dl2A-local.pw.a2m.gz 1dl2A/1dl2A-T0120-116-210-local.pw.a2m.gz \ 1dl2A/T0120-116-210-1dl2A-2track-local.pw.a2m.gz \ 1dl2A/T0120-116-210-1dl2A-2track-global.pw.a2m.gz \ 1dl2A/T0120-116-210-1dl2A-vit.pw.a2m.gz 1dl2A/1dl2A-T0120-116-210-vit.pw.a2m.gz \ 1dl2A/T0120-116-210-1dl2A-global.pw.a2m.gz 1dl2A/1dl2A-T0120-116-210-global.pw.a2m.gz \ 1dl2A/1dl2A-T0120-116-210-fssp-global.pw.a2m.gz \ 1dl2A/xxxx-1dl2A-T0120-116-210-local.pw.a2m.gz 1dl2A/xxxx-1dl2A-T0120-116-210-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1dl2A/info/1dl2A.stride-mixed.seq', needed by `1dl2A/T0120-116-210-1dl2A-local.pw.a2m.gz'. make[2]: Target `1dl2A/T0120-116-210-1dl2A-local.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1dl2A/nostruct-align/1dl2A.t99-w0.5.mod', needed by `1dl2A/1dl2A-T0120-116-210-local.pw.a2m.gz'. make[2]: Target `1dl2A/1dl2A-T0120-116-210-local.pw.a2m.gz' not remade because of errors. echo ReadNeuralNet /projects/compbio/usr/karplus/predict-2nd/testing/networks/overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net > tmp.script echo ReadA2M T0120-116-210.remote-t2k.a2m.gz >> tmp.script echo PrintPrediction T0120-116-210.remote-t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0120-116-210.remote-t2k.2d.seq >> tmp.script echo PrintRDB T0120-116-210.remote-t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net # command:# Reading A2M format from T0120-116-210.remote-t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0120-116-210.remote-t2k.a2m with 8 sequences, total weight= 5.05436 avg weight= 0.631795 35 iterations Regularizing alignment for T0120-116-210.remote-t2k.a2m.gz # After reading T0120-116-210.remote-t2k.a2m.gz, have 95 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0120-116-210.remote-t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0120-116-210.remote-t2k.2d.seq # command:# Network initialization done # Printing prediction to T0120-116-210.remote-t2k.2d.rdb # command:rm tmp.script /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0120-116-210.remote-t2k.2d.rdb T0120-116-210.remote-t2k-2d.mod make[2]: Target `1dl2A/T0120-116-210-1dl2A-2track-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1dl2A/T0120-116-210-1dl2A-2track-global.pw.a2m.gz' not remade because of errors. make[2]: Target `1dl2A/T0120-116-210-1dl2A-vit.pw.a2m.gz' not remade because of errors. make[2]: Target `1dl2A/1dl2A-T0120-116-210-vit.pw.a2m.gz' not remade because of errors. make[2]: Target `1dl2A/T0120-116-210-1dl2A-global.pw.a2m.gz' not remade because of errors. make[2]: Target `1dl2A/1dl2A-T0120-116-210-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1dl2A/struct-align/1dl2A.fssp-w0.5.mod', needed by `1dl2A/1dl2A-T0120-116-210-fssp-global.pw.a2m.gz'. make[2]: Target `1dl2A/1dl2A-T0120-116-210-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dl2A/xxxx-1dl2A-T0120-116-210-local.pw.a2m.gz'. make[2]: Target `1dl2A/xxxx-1dl2A-T0120-116-210-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1dl2A/xxxx-1dl2A-T0120-116-210-global.pw.a2m.gz' not remade because of errors. rm T0120-116-210.remote-t2k.2d.rdb make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make: [joints] Error 2 (ignored) make -k PRED=1hsm PRED2=1h A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make -k \ 1hsm/T0120-116-210-1hsm-local.pw.a2m.gz 1hsm/1hsm-T0120-116-210-local.pw.a2m.gz \ 1hsm/T0120-116-210-1hsm-2track-local.pw.a2m.gz \ 1hsm/T0120-116-210-1hsm-2track-global.pw.a2m.gz \ 1hsm/T0120-116-210-1hsm-vit.pw.a2m.gz 1hsm/1hsm-T0120-116-210-vit.pw.a2m.gz \ 1hsm/T0120-116-210-1hsm-global.pw.a2m.gz 1hsm/1hsm-T0120-116-210-global.pw.a2m.gz \ 1hsm/1hsm-T0120-116-210-fssp-global.pw.a2m.gz \ 1hsm/xxxx-1hsm-T0120-116-210-local.pw.a2m.gz 1hsm/xxxx-1hsm-T0120-116-210-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' mkdir 1hsm fixmode 1hsm make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/T0120-116-210-1hsm-local.pw -i T0120-116-210.remote-t2k-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-116-210.remote-t2k-w0.5.mod T0120-116-210.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.248413 Database has 3 sequences with 253 residues. gzip -f 1hsm/T0120-116-210-1hsm-local.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/1hsm-T0120-116-210-local.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18768/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.646412 Database has 3 sequences with 253 residues. gzip -f 1hsm/1hsm-T0120-116-210-local.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/T0120-116-210-1hsm-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-116-210.remote-t2k-w0.5.mod,T0120-116-210.remote-t2k-2d.mod \ -db T0120-116-210.seq,T0120-116-210.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 T0120-116-210.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m T0120-116-210.remote-t2k-2d.mod(599): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-116-210.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.481903 Database has 3 sequences with 253 residues. gzip -f 1hsm/T0120-116-210-1hsm-2track-local.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/T0120-116-210-1hsm-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-116-210.remote-t2k-w0.5.mod,T0120-116-210.remote-t2k-2d.mod \ -db T0120-116-210.seq,T0120-116-210.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0120-116-210.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m T0120-116-210.remote-t2k-2d.mod(599): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-116-210.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -41.100830 Database has 3 sequences with 253 residues. gzip -f 1hsm/T0120-116-210-1hsm-2track-global.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/T0120-116-210-1hsm-vit.pw \ -i T0120-116-210.remote-t2k-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-116-210.remote-t2k-w0.5.mod T0120-116-210.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.911411 Database has 3 sequences with 253 residues. gzip -f 1hsm/T0120-116-210-1hsm-vit.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/1hsm-T0120-116-210-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18768/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.383747 Database has 3 sequences with 253 residues. gzip -f 1hsm/1hsm-T0120-116-210-vit.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/T0120-116-210-1hsm-global.pw -i T0120-116-210.remote-t2k-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-116-210.remote-t2k-w0.5.mod T0120-116-210.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.418331 Database has 3 sequences with 253 residues. gzip -f 1hsm/T0120-116-210-1hsm-global.pw.a2m make 1hsm make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `1hsm' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 1hsm/1hsm-T0120-116-210-global.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hsm/info/1hsm.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1h/1hsm/nostruct-align/1hsm.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18768/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.424332 Database has 3 sequences with 253 residues. gzip -f 1hsm/1hsm-T0120-116-210-global.pw.a2m make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hsm/struct-align/1hsm.fssp-w0.5.mod', needed by `1hsm/1hsm-T0120-116-210-fssp-global.pw.a2m.gz'. make[2]: Target `1hsm/1hsm-T0120-116-210-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hsm/xxxx-1hsm-T0120-116-210-local.pw.a2m.gz'. make[2]: Target `1hsm/xxxx-1hsm-T0120-116-210-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1hsm/xxxx-1hsm-T0120-116-210-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make: [joints] Error 2 (ignored) make -k PRED=2kinB PRED2=2k A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make -k \ 2kinB/T0120-116-210-2kinB-local.pw.a2m.gz 2kinB/2kinB-T0120-116-210-local.pw.a2m.gz \ 2kinB/T0120-116-210-2kinB-2track-local.pw.a2m.gz \ 2kinB/T0120-116-210-2kinB-2track-global.pw.a2m.gz \ 2kinB/T0120-116-210-2kinB-vit.pw.a2m.gz 2kinB/2kinB-T0120-116-210-vit.pw.a2m.gz \ 2kinB/T0120-116-210-2kinB-global.pw.a2m.gz 2kinB/2kinB-T0120-116-210-global.pw.a2m.gz \ 2kinB/2kinB-T0120-116-210-fssp-global.pw.a2m.gz \ 2kinB/xxxx-2kinB-T0120-116-210-local.pw.a2m.gz 2kinB/xxxx-2kinB-T0120-116-210-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' mkdir 2kinB fixmode 2kinB make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/T0120-116-210-2kinB-local.pw -i T0120-116-210.remote-t2k-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-116-210.remote-t2k-w0.5.mod T0120-116-210.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.271923 Database has 3 sequences with 295 residues. gzip -f 2kinB/T0120-116-210-2kinB-local.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/2kinB-T0120-116-210-local.pw -i /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13821/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.661922 Database has 3 sequences with 295 residues. gzip -f 2kinB/2kinB-T0120-116-210-local.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/T0120-116-210-2kinB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-116-210.remote-t2k-w0.5.mod,T0120-116-210.remote-t2k-2d.mod \ -db T0120-116-210.seq,T0120-116-210.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq,/projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 T0120-116-210.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m T0120-116-210.remote-t2k-2d.mod(599): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-116-210.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.716091 Database has 3 sequences with 295 residues. gzip -f 2kinB/T0120-116-210-2kinB-2track-local.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/T0120-116-210-2kinB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-116-210.remote-t2k-w0.5.mod,T0120-116-210.remote-t2k-2d.mod \ -db T0120-116-210.seq,T0120-116-210.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq,/projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0120-116-210.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m T0120-116-210.remote-t2k-2d.mod(599): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-116-210.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.989494 Database has 3 sequences with 295 residues. gzip -f 2kinB/T0120-116-210-2kinB-2track-global.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/T0120-116-210-2kinB-vit.pw \ -i T0120-116-210.remote-t2k-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-116-210.remote-t2k-w0.5.mod T0120-116-210.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.957596 Database has 3 sequences with 295 residues. gzip -f 2kinB/T0120-116-210-2kinB-vit.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/2kinB-T0120-116-210-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13821/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.294598 Database has 3 sequences with 295 residues. gzip -f 2kinB/2kinB-T0120-116-210-vit.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/T0120-116-210-2kinB-global.pw -i T0120-116-210.remote-t2k-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-116-210.remote-t2k-w0.5.mod T0120-116-210.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29511/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -39.320320 Database has 3 sequences with 295 residues. gzip -f 2kinB/T0120-116-210-2kinB-global.pw.a2m make 2kinB make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' make[3]: `2kinB' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-116-210' /projects/compbio/bin/alpha.new/hmmscore 2kinB/2kinB-T0120-116-210-global.pw -i /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod -db T0120-116-210.seq -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2k/2kinB/info/2kinB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2k/2kinB/nostruct-align/2kinB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13821/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.677013 Database has 3 sequences with 295 residues. gzip -f 2kinB/2kinB-T0120-116-210-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2k/2kinB/struct-align/2kinB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2k/2kinB/struct-align/2kinB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31687 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31687/tmp -alignfile /projects/compbio/experiments/models.97/pdb/2k/2kinB/struct-align/2kinB.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/2k/2kinB/struct-align/2kinB.fssp.a2m.gz (3 sequences, 100 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31687/tmp.a2m. Dropping 2 (of 3) sequences with > 80.0% id 1 sequences left after dropping 2 of 3 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31687/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31687/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31687/tmp.a2m (1 sequences, 100 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31687/tmp.mod /projects/compbio/experiments/models.97/pdb/2k/2kinB/struct-align/2kinB.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31687 80.0% id 11 sequences left after dropping 6 of 17 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13440/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13440/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13440/tmp.a2m (11 sequences, 132 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13440/tmp.mod /projects/compbio/experiments/models.97/pdb/1n/1nfn/struct-align/1nfn.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13440 80.0% id 4 sequences left after dropping 2 of 6 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15006/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15006/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15006/tmp.a2m (4 sequences, 149 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15006/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cwpA/struct-align/1cwpA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15006