echo template template make -k PRED=1dar PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make -k \ 1dar/T0124-1dar-local.pw.a2m.gz 1dar/1dar-T0124-local.pw.a2m.gz \ 1dar/T0124-1dar-2track-local.pw.a2m.gz \ 1dar/T0124-1dar-2track-global.pw.a2m.gz \ 1dar/T0124-1dar-vit.pw.a2m.gz 1dar/1dar-T0124-vit.pw.a2m.gz \ 1dar/T0124-1dar-global.pw.a2m.gz 1dar/1dar-T0124-global.pw.a2m.gz \ 1dar/1dar-T0124-fssp-global.pw.a2m.gz \ 1dar/xxxx-1dar-T0124-local.pw.a2m.gz 1dar/xxxx-1dar-T0124-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' mkdir 1dar fixmode 1dar make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/T0124-1dar-local.pw -i T0124.t2k-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0124.t2k-w0.5.mod T0124.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/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: -76.158768 Database has 3 sequences with 1548 residues. gzip -f 1dar/T0124-1dar-local.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/1dar-T0124-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5072/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: -361.871094 Database has 3 sequences with 1548 residues. gzip -f 1dar/1dar-T0124-local.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/T0124-1dar-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0124.t2k-w0.5.mod,T0124.t2k-2d.mod \ -db T0124.seq,T0124.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.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 T0124.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/tmp.a2m T0124.t2k-2d.mod(1481): Reading track 1 model from MODEL -- Model from 2nd structure file T0124.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -76.670776 Database has 3 sequences with 1548 residues. gzip -f 1dar/T0124-1dar-2track-local.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/T0124-1dar-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0124.t2k-w0.5.mod,T0124.t2k-2d.mod \ -db T0124.seq,T0124.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.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. T0124.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/tmp.a2m T0124.t2k-2d.mod(1481): Reading track 1 model from MODEL -- Model from 2nd structure file T0124.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.183666 Database has 3 sequences with 1548 residues. gzip -f 1dar/T0124-1dar-2track-global.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/T0124-1dar-vit.pw \ -i T0124.t2k-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0124.t2k-w0.5.mod T0124.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/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: -70.405075 Database has 3 sequences with 1548 residues. gzip -f 1dar/T0124-1dar-vit.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/1dar-T0124-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5072/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: -358.195435 Database has 3 sequences with 1548 residues. gzip -f 1dar/1dar-T0124-vit.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/T0124-1dar-global.pw -i T0124.t2k-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0124.t2k-w0.5.mod T0124.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/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: -64.640656 Database has 3 sequences with 1548 residues. gzip -f 1dar/T0124-1dar-global.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/1dar-T0124-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dar/nostruct-align/1dar.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5072/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: -356.897003 Database has 3 sequences with 1548 residues. gzip -f 1dar/1dar-T0124-global.pw.a2m make 1dar make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1dar' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1dar/1dar-T0124-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dar/struct-align/1dar.fssp-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dar/info/1dar.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dar/struct-align/1dar.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dar/struct-align/1dar.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25190/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: -386.912323 Database has 3 sequences with 1548 residues. gzip -f 1dar/1dar-T0124-fssp-global.pw.a2m make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dar/xxxx-1dar-T0124-local.pw.a2m.gz'. make[2]: Target `1dar/xxxx-1dar-T0124-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1dar/xxxx-1dar-T0124-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' make: [joints] Error 2 (ignored) echo target target make -k PRED=1a6o PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make -k \ 1a6o/T0124-1a6o-local.pw.a2m.gz 1a6o/1a6o-T0124-local.pw.a2m.gz \ 1a6o/T0124-1a6o-2track-local.pw.a2m.gz \ 1a6o/T0124-1a6o-2track-global.pw.a2m.gz \ 1a6o/T0124-1a6o-vit.pw.a2m.gz 1a6o/1a6o-T0124-vit.pw.a2m.gz \ 1a6o/T0124-1a6o-global.pw.a2m.gz 1a6o/1a6o-T0124-global.pw.a2m.gz \ 1a6o/1a6o-T0124-fssp-global.pw.a2m.gz \ 1a6o/xxxx-1a6o-T0124-local.pw.a2m.gz 1a6o/xxxx-1a6o-T0124-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' mkdir 1a6o fixmode 1a6o make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/T0124-1a6o-local.pw -i T0124.t2k-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0124.t2k-w0.5.mod T0124.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/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: -77.021652 Database has 3 sequences with 901 residues. gzip -f 1a6o/T0124-1a6o-local.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/1a6o-T0124-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12373/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: -143.285995 Database has 3 sequences with 901 residues. gzip -f 1a6o/1a6o-T0124-local.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/T0124-1a6o-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0124.t2k-w0.5.mod,T0124.t2k-2d.mod \ -db T0124.seq,T0124.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.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 T0124.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/tmp.a2m T0124.t2k-2d.mod(1481): Reading track 1 model from MODEL -- Model from 2nd structure file T0124.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -76.324150 Database has 3 sequences with 901 residues. gzip -f 1a6o/T0124-1a6o-2track-local.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/T0124-1a6o-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0124.t2k-w0.5.mod,T0124.t2k-2d.mod \ -db T0124.seq,T0124.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.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. T0124.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/tmp.a2m T0124.t2k-2d.mod(1481): Reading track 1 model from MODEL -- Model from 2nd structure file T0124.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.604832 Database has 3 sequences with 901 residues. gzip -f 1a6o/T0124-1a6o-2track-global.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/T0124-1a6o-vit.pw \ -i T0124.t2k-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0124.t2k-w0.5.mod T0124.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/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: -70.968338 Database has 3 sequences with 901 residues. gzip -f 1a6o/T0124-1a6o-vit.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/1a6o-T0124-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12373/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: -137.502640 Database has 3 sequences with 901 residues. gzip -f 1a6o/1a6o-T0124-vit.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/T0124-1a6o-global.pw -i T0124.t2k-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0124.t2k-w0.5.mod T0124.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/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: -59.612659 Database has 3 sequences with 901 residues. gzip -f 1a6o/T0124-1a6o-global.pw.a2m make 1a6o make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t124' make[3]: `1a6o' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t124' /projects/compbio/bin/alpha.new/hmmscore 1a6o/1a6o-T0124-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod -db T0124.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a6o/info/1a6o.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a6o/nostruct-align/1a6o.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12373/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: -135.939987 Database has 3 sequences with 901 residues. gzip -f 1a6o/1a6o-T0124-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a6o/struct-align/1a6o.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a6o/struct-align/1a6o.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21785 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21785/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a6o/struct-align/1a6o.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/1a/1a6o/struct-align/1a6o.fssp.a2m.gz (14 sequences, 327 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21785/tmp.a2m. Dropping 2 (of 14) duplicate sequences with differing IDs Dropping 4 (of 14) sequences with > 80.0% id 8 sequences left after dropping 6 of 14 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21785/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21785/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-21785/tmp.a2m (8 sequences, 327 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21785/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a6o/struct-align/1a6o.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21785 80.0% id 9 sequences left after dropping 31 of 40 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29982/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29982/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-29982/tmp.a2m (9 sequences, 328 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29982/tmp.mod /projects/compbio/experiments/models.97/pdb/1n/1nnt/struct-align/1nnt.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29982 80.0% id 5 sequences left after dropping 19 of 24 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27810/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27810/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-27810/tmp.a2m (5 sequences, 385 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27810/tmp.mod /projects/compbio/experiments/models.97/pdb/3m/3mdeA/struct-align/3mdeA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27810 80.0% id 7 sequences left after dropping 10 of 17 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27886/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27886/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-27886/tmp.a2m (7 sequences, 639 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27886/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cx8B/struct-align/1cx8B.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27886 80.0% id 8 sequences left after dropping 1 of 9 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23972/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23972/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-23972/tmp.a2m (8 sequences, 917 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23972/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qu2A/struct-align/1qu2A.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23972 80.0% id 105 sequences left after dropping 12 of 117 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27989/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27989/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-27989/tmp.a2m (105 sequences, 727 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27989/tmp.mod /projects/compbio/experiments/models.97/pdb/1r/1reqA/struct-align/1reqA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27989 80.0% id 22 sequences left after dropping 2 of 24 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23778/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23778/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-23778/tmp.a2m (22 sequences, 544 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23778/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a36A/struct-align/1a36A.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23778