echo 3.64.1 3.64.1 make -k PRED=1a8q PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1a8q/T0126-1a8q-local.pw.a2m.gz 1a8q/1a8q-T0126-local.pw.a2m.gz \ 1a8q/T0126-1a8q-2track-local.pw.a2m.gz \ 1a8q/T0126-1a8q-2track-global.pw.a2m.gz \ 1a8q/T0126-1a8q-vit.pw.a2m.gz 1a8q/1a8q-T0126-vit.pw.a2m.gz \ 1a8q/T0126-1a8q-global.pw.a2m.gz 1a8q/1a8q-T0126-global.pw.a2m.gz \ 1a8q/1a8q-T0126-fssp-global.pw.a2m.gz \ 1a8q/xxxx-1a8q-T0126-local.pw.a2m.gz 1a8q/xxxx-1a8q-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1a8q/T0126-1a8q-local.pw.a2m.gz' is up to date. make[2]: `1a8q/1a8q-T0126-local.pw.a2m.gz' is up to date. make[2]: `1a8q/T0126-1a8q-2track-local.pw.a2m.gz' is up to date. make[2]: `1a8q/T0126-1a8q-2track-global.pw.a2m.gz' is up to date. make[2]: `1a8q/T0126-1a8q-vit.pw.a2m.gz' is up to date. make[2]: `1a8q/1a8q-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1a8q/T0126-1a8q-global.pw.a2m.gz' is up to date. make[2]: `1a8q/1a8q-T0126-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a8q/struct-align/1a8q.fssp-w0.5.mod', needed by `1a8q/1a8q-T0126-fssp-global.pw.a2m.gz'. make[2]: Target `1a8q/1a8q-T0126-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a8q/xxxx-1a8q-T0126-local.pw.a2m.gz'. make[2]: Target `1a8q/xxxx-1a8q-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1a8q/xxxx-1a8q-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) make -k PRED=1qtrA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1qtrA/T0126-1qtrA-local.pw.a2m.gz 1qtrA/1qtrA-T0126-local.pw.a2m.gz \ 1qtrA/T0126-1qtrA-2track-local.pw.a2m.gz \ 1qtrA/T0126-1qtrA-2track-global.pw.a2m.gz \ 1qtrA/T0126-1qtrA-vit.pw.a2m.gz 1qtrA/1qtrA-T0126-vit.pw.a2m.gz \ 1qtrA/T0126-1qtrA-global.pw.a2m.gz 1qtrA/1qtrA-T0126-global.pw.a2m.gz \ 1qtrA/1qtrA-T0126-fssp-global.pw.a2m.gz \ 1qtrA/xxxx-1qtrA-T0126-local.pw.a2m.gz 1qtrA/xxxx-1qtrA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1qtrA/T0126-1qtrA-local.pw.a2m.gz' is up to date. make[2]: `1qtrA/1qtrA-T0126-local.pw.a2m.gz' is up to date. make[2]: `1qtrA/T0126-1qtrA-2track-local.pw.a2m.gz' is up to date. make[2]: `1qtrA/T0126-1qtrA-2track-global.pw.a2m.gz' is up to date. make[2]: `1qtrA/T0126-1qtrA-vit.pw.a2m.gz' is up to date. make[2]: `1qtrA/1qtrA-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1qtrA/T0126-1qtrA-global.pw.a2m.gz' is up to date. make[2]: `1qtrA/1qtrA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1qtrA/1qtrA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtrA/xxxx-1qtrA-T0126-local.pw.a2m.gz'. make[2]: Target `1qtrA/xxxx-1qtrA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1qtrA/xxxx-1qtrA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) make -k PRED=1jfrA PRED2=1j joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1jfrA/T0126-1jfrA-local.pw.a2m.gz 1jfrA/1jfrA-T0126-local.pw.a2m.gz \ 1jfrA/T0126-1jfrA-2track-local.pw.a2m.gz \ 1jfrA/T0126-1jfrA-2track-global.pw.a2m.gz \ 1jfrA/T0126-1jfrA-vit.pw.a2m.gz 1jfrA/1jfrA-T0126-vit.pw.a2m.gz \ 1jfrA/T0126-1jfrA-global.pw.a2m.gz 1jfrA/1jfrA-T0126-global.pw.a2m.gz \ 1jfrA/1jfrA-T0126-fssp-global.pw.a2m.gz \ 1jfrA/xxxx-1jfrA-T0126-local.pw.a2m.gz 1jfrA/xxxx-1jfrA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1jfrA/T0126-1jfrA-local.pw.a2m.gz' is up to date. make[2]: `1jfrA/1jfrA-T0126-local.pw.a2m.gz' is up to date. make[2]: `1jfrA/T0126-1jfrA-2track-local.pw.a2m.gz' is up to date. make[2]: `1jfrA/T0126-1jfrA-2track-global.pw.a2m.gz' is up to date. make[2]: `1jfrA/T0126-1jfrA-vit.pw.a2m.gz' is up to date. make[2]: `1jfrA/1jfrA-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1jfrA/T0126-1jfrA-global.pw.a2m.gz' is up to date. make[2]: `1jfrA/1jfrA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1jfrA/1jfrA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1jfrA/xxxx-1jfrA-T0126-local.pw.a2m.gz'. make[2]: Target `1jfrA/xxxx-1jfrA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1jfrA/xxxx-1jfrA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.61.1 3.61.1 make -k PRED=1ej0A PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1ej0A/T0126-1ej0A-local.pw.a2m.gz 1ej0A/1ej0A-T0126-local.pw.a2m.gz \ 1ej0A/T0126-1ej0A-2track-local.pw.a2m.gz \ 1ej0A/T0126-1ej0A-2track-global.pw.a2m.gz \ 1ej0A/T0126-1ej0A-vit.pw.a2m.gz 1ej0A/1ej0A-T0126-vit.pw.a2m.gz \ 1ej0A/T0126-1ej0A-global.pw.a2m.gz 1ej0A/1ej0A-T0126-global.pw.a2m.gz \ 1ej0A/1ej0A-T0126-fssp-global.pw.a2m.gz \ 1ej0A/xxxx-1ej0A-T0126-local.pw.a2m.gz 1ej0A/xxxx-1ej0A-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' mkdir 1ej0A fixmode 1ej0A make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-local.pw -i T0126.t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.t2k-w0.5.mod T0126.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21291/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: -83.316109 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-local.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/1ej0A-T0126-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-31366/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: -102.396446 Database has 3 sequences with 523 residues. gzip -f 1ej0A/1ej0A-T0126-local.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.t2k-w0.5.mod,T0126.t2k-2d.mod \ -db T0126.seq,T0126.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.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 T0126.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21291/tmp.a2m T0126.t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -71.223099 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-2track-local.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.t2k-w0.5.mod,T0126.t2k-2d.mod \ -db T0126.seq,T0126.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.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. T0126.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21291/tmp.a2m T0126.t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -60.468662 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-2track-global.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-vit.pw \ -i T0126.t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.t2k-w0.5.mod T0126.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21291/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: -79.210098 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-vit.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/1ej0A-T0126-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-31366/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: -99.333107 Database has 3 sequences with 523 residues. gzip -f 1ej0A/1ej0A-T0126-vit.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-global.pw -i T0126.t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.t2k-w0.5.mod T0126.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21291/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: -71.158646 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-global.pw.a2m make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/1ej0A-T0126-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ej0A/nostruct-align/1ej0A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-31366/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: -99.918327 Database has 3 sequences with 523 residues. gzip -f 1ej0A/1ej0A-T0126-global.pw.a2m make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1ej0A/struct-align/1ej0A.fssp-w0.5.mod', needed by `1ej0A/1ej0A-T0126-fssp-global.pw.a2m.gz'. make[2]: Target `1ej0A/1ej0A-T0126-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ej0A/xxxx-1ej0A-T0126-local.pw.a2m.gz'. make[2]: Target `1ej0A/xxxx-1ej0A-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1ej0A/xxxx-1ej0A-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.57.2 3.57.2 make -k PRED=1atzA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1atzA/T0126-1atzA-local.pw.a2m.gz 1atzA/1atzA-T0126-local.pw.a2m.gz \ 1atzA/T0126-1atzA-2track-local.pw.a2m.gz \ 1atzA/T0126-1atzA-2track-global.pw.a2m.gz \ 1atzA/T0126-1atzA-vit.pw.a2m.gz 1atzA/1atzA-T0126-vit.pw.a2m.gz \ 1atzA/T0126-1atzA-global.pw.a2m.gz 1atzA/1atzA-T0126-global.pw.a2m.gz \ 1atzA/1atzA-T0126-fssp-global.pw.a2m.gz \ 1atzA/xxxx-1atzA-T0126-local.pw.a2m.gz 1atzA/xxxx-1atzA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1atzA/T0126-1atzA-local.pw.a2m.gz' is up to date. make[2]: `1atzA/1atzA-T0126-local.pw.a2m.gz' is up to date. make[2]: `1atzA/T0126-1atzA-2track-local.pw.a2m.gz' is up to date. make[2]: `1atzA/T0126-1atzA-2track-global.pw.a2m.gz' is up to date. make[2]: `1atzA/T0126-1atzA-vit.pw.a2m.gz' is up to date. make[2]: `1atzA/1atzA-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1atzA/T0126-1atzA-global.pw.a2m.gz' is up to date. make[2]: `1atzA/1atzA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1atzA/1atzA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1atzA/xxxx-1atzA-T0126-local.pw.a2m.gz'. make[2]: Target `1atzA/xxxx-1atzA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1atzA/xxxx-1atzA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.1.3 3.1.3 make -k PRED=2tpsA PRED2=2t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 2tpsA/T0126-2tpsA-local.pw.a2m.gz 2tpsA/2tpsA-T0126-local.pw.a2m.gz \ 2tpsA/T0126-2tpsA-2track-local.pw.a2m.gz \ 2tpsA/T0126-2tpsA-2track-global.pw.a2m.gz \ 2tpsA/T0126-2tpsA-vit.pw.a2m.gz 2tpsA/2tpsA-T0126-vit.pw.a2m.gz \ 2tpsA/T0126-2tpsA-global.pw.a2m.gz 2tpsA/2tpsA-T0126-global.pw.a2m.gz \ 2tpsA/2tpsA-T0126-fssp-global.pw.a2m.gz \ 2tpsA/xxxx-2tpsA-T0126-local.pw.a2m.gz 2tpsA/xxxx-2tpsA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `2tpsA/T0126-2tpsA-local.pw.a2m.gz' is up to date. make[2]: `2tpsA/2tpsA-T0126-local.pw.a2m.gz' is up to date. make[2]: `2tpsA/T0126-2tpsA-2track-local.pw.a2m.gz' is up to date. make[2]: `2tpsA/T0126-2tpsA-2track-global.pw.a2m.gz' is up to date. make[2]: `2tpsA/T0126-2tpsA-vit.pw.a2m.gz' is up to date. make[2]: `2tpsA/2tpsA-T0126-vit.pw.a2m.gz' is up to date. make[2]: `2tpsA/T0126-2tpsA-global.pw.a2m.gz' is up to date. make[2]: `2tpsA/2tpsA-T0126-global.pw.a2m.gz' is up to date. make[2]: `2tpsA/2tpsA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2tpsA/xxxx-2tpsA-T0126-local.pw.a2m.gz'. make[2]: Target `2tpsA/xxxx-2tpsA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `2tpsA/xxxx-2tpsA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 1.47.1,3.42.1 1.47.1,3.42.1 make -k PRED=1pgtA PRED2=1p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1pgtA/T0126-1pgtA-local.pw.a2m.gz 1pgtA/1pgtA-T0126-local.pw.a2m.gz \ 1pgtA/T0126-1pgtA-2track-local.pw.a2m.gz \ 1pgtA/T0126-1pgtA-2track-global.pw.a2m.gz \ 1pgtA/T0126-1pgtA-vit.pw.a2m.gz 1pgtA/1pgtA-T0126-vit.pw.a2m.gz \ 1pgtA/T0126-1pgtA-global.pw.a2m.gz 1pgtA/1pgtA-T0126-global.pw.a2m.gz \ 1pgtA/1pgtA-T0126-fssp-global.pw.a2m.gz \ 1pgtA/xxxx-1pgtA-T0126-local.pw.a2m.gz 1pgtA/xxxx-1pgtA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1pgtA/T0126-1pgtA-local.pw.a2m.gz' is up to date. make[2]: `1pgtA/1pgtA-T0126-local.pw.a2m.gz' is up to date. make[2]: `1pgtA/T0126-1pgtA-2track-local.pw.a2m.gz' is up to date. make[2]: `1pgtA/T0126-1pgtA-2track-global.pw.a2m.gz' is up to date. make[2]: `1pgtA/T0126-1pgtA-vit.pw.a2m.gz' is up to date. make[2]: `1pgtA/1pgtA-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1pgtA/T0126-1pgtA-global.pw.a2m.gz' is up to date. make[2]: `1pgtA/1pgtA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1pgtA/1pgtA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pgtA/xxxx-1pgtA-T0126-local.pw.a2m.gz'. make[2]: Target `1pgtA/xxxx-1pgtA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1pgtA/xxxx-1pgtA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.67.1 3.67.1 make -k PRED=1bx4A PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1bx4A/T0126-1bx4A-local.pw.a2m.gz 1bx4A/1bx4A-T0126-local.pw.a2m.gz \ 1bx4A/T0126-1bx4A-2track-local.pw.a2m.gz \ 1bx4A/T0126-1bx4A-2track-global.pw.a2m.gz \ 1bx4A/T0126-1bx4A-vit.pw.a2m.gz 1bx4A/1bx4A-T0126-vit.pw.a2m.gz \ 1bx4A/T0126-1bx4A-global.pw.a2m.gz 1bx4A/1bx4A-T0126-global.pw.a2m.gz \ 1bx4A/1bx4A-T0126-fssp-global.pw.a2m.gz \ 1bx4A/xxxx-1bx4A-T0126-local.pw.a2m.gz 1bx4A/xxxx-1bx4A-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1bx4A/T0126-1bx4A-local.pw.a2m.gz' is up to date. make[2]: `1bx4A/1bx4A-T0126-local.pw.a2m.gz' is up to date. make[2]: `1bx4A/T0126-1bx4A-2track-local.pw.a2m.gz' is up to date. make[2]: `1bx4A/T0126-1bx4A-2track-global.pw.a2m.gz' is up to date. make[2]: `1bx4A/T0126-1bx4A-vit.pw.a2m.gz' is up to date. make[2]: `1bx4A/1bx4A-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1bx4A/T0126-1bx4A-global.pw.a2m.gz' is up to date. make[2]: `1bx4A/1bx4A-T0126-global.pw.a2m.gz' is up to date. make[2]: `1bx4A/1bx4A-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bx4A/xxxx-1bx4A-T0126-local.pw.a2m.gz'. make[2]: Target `1bx4A/xxxx-1bx4A-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1bx4A/xxxx-1bx4A-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 2.2.3 2.2.3 make -k PRED=1pdkB PRED2=1p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1pdkB/T0126-1pdkB-local.pw.a2m.gz 1pdkB/1pdkB-T0126-local.pw.a2m.gz \ 1pdkB/T0126-1pdkB-2track-local.pw.a2m.gz \ 1pdkB/T0126-1pdkB-2track-global.pw.a2m.gz \ 1pdkB/T0126-1pdkB-vit.pw.a2m.gz 1pdkB/1pdkB-T0126-vit.pw.a2m.gz \ 1pdkB/T0126-1pdkB-global.pw.a2m.gz 1pdkB/1pdkB-T0126-global.pw.a2m.gz \ 1pdkB/1pdkB-T0126-fssp-global.pw.a2m.gz \ 1pdkB/xxxx-1pdkB-T0126-local.pw.a2m.gz 1pdkB/xxxx-1pdkB-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[2]: `1pdkB/T0126-1pdkB-local.pw.a2m.gz' is up to date. make[2]: `1pdkB/1pdkB-T0126-local.pw.a2m.gz' is up to date. make[2]: `1pdkB/T0126-1pdkB-2track-local.pw.a2m.gz' is up to date. make[2]: `1pdkB/T0126-1pdkB-2track-global.pw.a2m.gz' is up to date. make[2]: `1pdkB/T0126-1pdkB-vit.pw.a2m.gz' is up to date. make[2]: `1pdkB/1pdkB-T0126-vit.pw.a2m.gz' is up to date. make[2]: `1pdkB/T0126-1pdkB-global.pw.a2m.gz' is up to date. make[2]: `1pdkB/1pdkB-T0126-global.pw.a2m.gz' is up to date. make[2]: `1pdkB/1pdkB-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pdkB/xxxx-1pdkB-T0126-local.pw.a2m.gz'. make[2]: Target `1pdkB/xxxx-1pdkB-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1pdkB/xxxx-1pdkB-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.64.1 3.64.1 make -k PRED=1a8q PRED2=1a A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1a8q/T0126-1a8q-local.pw.a2m.gz 1a8q/1a8q-T0126-local.pw.a2m.gz \ 1a8q/T0126-1a8q-2track-local.pw.a2m.gz \ 1a8q/T0126-1a8q-2track-global.pw.a2m.gz \ 1a8q/T0126-1a8q-vit.pw.a2m.gz 1a8q/1a8q-T0126-vit.pw.a2m.gz \ 1a8q/T0126-1a8q-global.pw.a2m.gz 1a8q/1a8q-T0126-global.pw.a2m.gz \ 1a8q/1a8q-T0126-fssp-global.pw.a2m.gz \ 1a8q/xxxx-1a8q-T0126-local.pw.a2m.gz 1a8q/xxxx-1a8q-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1a8q make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1a8q' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1a8q/T0126-1a8q-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -67.796341 Database has 3 sequences with 711 residues. gzip -f 1a8q/T0126-1a8q-local.pw.a2m make[2]: `1a8q/1a8q-T0126-local.pw.a2m.gz' is up to date. /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0126.remoter-t2k.2d.rdb T0126.remoter-t2k-2d.mod make 1a8q make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1a8q' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1a8q/T0126-1a8q-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1a8q/T0126-1a8q-2track-local.pw.a2m.gz] Error 1 make 1a8q make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1a8q' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1a8q/T0126-1a8q-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1a8q/T0126-1a8q-2track-global.pw.a2m.gz] Error 1 make 1a8q make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1a8q' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1a8q/T0126-1a8q-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -63.581989 Database has 3 sequences with 711 residues. gzip -f 1a8q/T0126-1a8q-vit.pw.a2m make[2]: `1a8q/1a8q-T0126-vit.pw.a2m.gz' is up to date. make 1a8q make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1a8q' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1a8q/T0126-1a8q-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a8q/info/1a8q.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -39.141991 Database has 3 sequences with 711 residues. gzip -f 1a8q/T0126-1a8q-global.pw.a2m make[2]: `1a8q/1a8q-T0126-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a8q/struct-align/1a8q.fssp-w0.5.mod', needed by `1a8q/1a8q-T0126-fssp-global.pw.a2m.gz'. make[2]: Target `1a8q/1a8q-T0126-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a8q/xxxx-1a8q-T0126-local.pw.a2m.gz'. make[2]: Target `1a8q/xxxx-1a8q-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1a8q/xxxx-1a8q-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) make -k PRED=1qtrA PRED2=1q A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1qtrA/T0126-1qtrA-local.pw.a2m.gz 1qtrA/1qtrA-T0126-local.pw.a2m.gz \ 1qtrA/T0126-1qtrA-2track-local.pw.a2m.gz \ 1qtrA/T0126-1qtrA-2track-global.pw.a2m.gz \ 1qtrA/T0126-1qtrA-vit.pw.a2m.gz 1qtrA/1qtrA-T0126-vit.pw.a2m.gz \ 1qtrA/T0126-1qtrA-global.pw.a2m.gz 1qtrA/1qtrA-T0126-global.pw.a2m.gz \ 1qtrA/1qtrA-T0126-fssp-global.pw.a2m.gz \ 1qtrA/xxxx-1qtrA-T0126-local.pw.a2m.gz 1qtrA/xxxx-1qtrA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1qtrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1qtrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1qtrA/T0126-1qtrA-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -67.086166 Database has 3 sequences with 791 residues. gzip -f 1qtrA/T0126-1qtrA-local.pw.a2m make[2]: `1qtrA/1qtrA-T0126-local.pw.a2m.gz' is up to date. make 1qtrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1qtrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1qtrA/T0126-1qtrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1qtrA/T0126-1qtrA-2track-local.pw.a2m.gz] Error 1 make 1qtrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1qtrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1qtrA/T0126-1qtrA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1qtrA/T0126-1qtrA-2track-global.pw.a2m.gz] Error 1 make 1qtrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1qtrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1qtrA/T0126-1qtrA-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -63.051830 Database has 3 sequences with 791 residues. gzip -f 1qtrA/T0126-1qtrA-vit.pw.a2m make[2]: `1qtrA/1qtrA-T0126-vit.pw.a2m.gz' is up to date. make 1qtrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1qtrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1qtrA/T0126-1qtrA-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qtrA/info/1qtrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -29.290674 Database has 3 sequences with 791 residues. gzip -f 1qtrA/T0126-1qtrA-global.pw.a2m make[2]: `1qtrA/1qtrA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1qtrA/1qtrA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtrA/xxxx-1qtrA-T0126-local.pw.a2m.gz'. make[2]: Target `1qtrA/xxxx-1qtrA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1qtrA/xxxx-1qtrA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) make -k PRED=1jfrA PRED2=1j A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1jfrA/T0126-1jfrA-local.pw.a2m.gz 1jfrA/1jfrA-T0126-local.pw.a2m.gz \ 1jfrA/T0126-1jfrA-2track-local.pw.a2m.gz \ 1jfrA/T0126-1jfrA-2track-global.pw.a2m.gz \ 1jfrA/T0126-1jfrA-vit.pw.a2m.gz 1jfrA/1jfrA-T0126-vit.pw.a2m.gz \ 1jfrA/T0126-1jfrA-global.pw.a2m.gz 1jfrA/1jfrA-T0126-global.pw.a2m.gz \ 1jfrA/1jfrA-T0126-fssp-global.pw.a2m.gz \ 1jfrA/xxxx-1jfrA-T0126-local.pw.a2m.gz 1jfrA/xxxx-1jfrA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1jfrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1jfrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1jfrA/T0126-1jfrA-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -67.007072 Database has 3 sequences with 685 residues. gzip -f 1jfrA/T0126-1jfrA-local.pw.a2m make[2]: `1jfrA/1jfrA-T0126-local.pw.a2m.gz' is up to date. make 1jfrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1jfrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1jfrA/T0126-1jfrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1jfrA/T0126-1jfrA-2track-local.pw.a2m.gz] Error 1 make 1jfrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1jfrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1jfrA/T0126-1jfrA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1jfrA/T0126-1jfrA-2track-global.pw.a2m.gz] Error 1 make 1jfrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1jfrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1jfrA/T0126-1jfrA-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -62.729736 Database has 3 sequences with 685 residues. gzip -f 1jfrA/T0126-1jfrA-vit.pw.a2m make[2]: `1jfrA/1jfrA-T0126-vit.pw.a2m.gz' is up to date. make 1jfrA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1jfrA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1jfrA/T0126-1jfrA-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1j/1jfrA/info/1jfrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -37.366661 Database has 3 sequences with 685 residues. gzip -f 1jfrA/T0126-1jfrA-global.pw.a2m make[2]: `1jfrA/1jfrA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1jfrA/1jfrA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1jfrA/xxxx-1jfrA-T0126-local.pw.a2m.gz'. make[2]: Target `1jfrA/xxxx-1jfrA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1jfrA/xxxx-1jfrA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) make -k PRED=1cr6B PRED2=1c A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1cr6B/T0126-1cr6B-local.pw.a2m.gz 1cr6B/1cr6B-T0126-local.pw.a2m.gz \ 1cr6B/T0126-1cr6B-2track-local.pw.a2m.gz \ 1cr6B/T0126-1cr6B-2track-global.pw.a2m.gz \ 1cr6B/T0126-1cr6B-vit.pw.a2m.gz 1cr6B/1cr6B-T0126-vit.pw.a2m.gz \ 1cr6B/T0126-1cr6B-global.pw.a2m.gz 1cr6B/1cr6B-T0126-global.pw.a2m.gz \ 1cr6B/1cr6B-T0126-fssp-global.pw.a2m.gz \ 1cr6B/xxxx-1cr6B-T0126-local.pw.a2m.gz 1cr6B/xxxx-1cr6B-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' mkdir 1cr6B fixmode 1cr6B make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0126-1cr6B-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -67.920227 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/T0126-1cr6B-local.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0126-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16293/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: -275.258545 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/1cr6B-T0126-local.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0126-1cr6B-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1cr6B/T0126-1cr6B-2track-local.pw.a2m.gz] Error 1 make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0126-1cr6B-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1cr6B/T0126-1cr6B-2track-global.pw.a2m.gz] Error 1 make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0126-1cr6B-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -64.356552 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/T0126-1cr6B-vit.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0126-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16293/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: -270.950562 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/1cr6B-T0126-vit.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0126-1cr6B-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: 4.332325 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/T0126-1cr6B-global.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0126-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16293/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: -269.993652 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/1cr6B-T0126-global.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0126-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.fssp-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6018/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: -317.920013 Database has 3 sequences with 1258 residues. gzip -f 1cr6B/1cr6B-T0126-fssp-global.pw.a2m make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cr6B/xxxx-1cr6B-T0126-local.pw.a2m.gz'. make[2]: Target `1cr6B/xxxx-1cr6B-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1cr6B/xxxx-1cr6B-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.61.1 3.61.1 make -k PRED=1ej0A PRED2=1e A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1ej0A/T0126-1ej0A-local.pw.a2m.gz 1ej0A/1ej0A-T0126-local.pw.a2m.gz \ 1ej0A/T0126-1ej0A-2track-local.pw.a2m.gz \ 1ej0A/T0126-1ej0A-2track-global.pw.a2m.gz \ 1ej0A/T0126-1ej0A-vit.pw.a2m.gz 1ej0A/1ej0A-T0126-vit.pw.a2m.gz \ 1ej0A/T0126-1ej0A-global.pw.a2m.gz 1ej0A/1ej0A-T0126-global.pw.a2m.gz \ 1ej0A/1ej0A-T0126-fssp-global.pw.a2m.gz \ 1ej0A/xxxx-1ej0A-T0126-local.pw.a2m.gz 1ej0A/xxxx-1ej0A-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -67.916428 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-local.pw.a2m make[2]: `1ej0A/1ej0A-T0126-local.pw.a2m.gz' is up to date. make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1ej0A/T0126-1ej0A-2track-local.pw.a2m.gz] Error 1 make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1ej0A/T0126-1ej0A-2track-global.pw.a2m.gz] Error 1 make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -64.241432 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-vit.pw.a2m make[2]: `1ej0A/1ej0A-T0126-vit.pw.a2m.gz' is up to date. make 1ej0A make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1ej0A' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1ej0A/T0126-1ej0A-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ej0A/info/1ej0A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -56.504669 Database has 3 sequences with 523 residues. gzip -f 1ej0A/T0126-1ej0A-global.pw.a2m make[2]: `1ej0A/1ej0A-T0126-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1ej0A/struct-align/1ej0A.fssp-w0.5.mod', needed by `1ej0A/1ej0A-T0126-fssp-global.pw.a2m.gz'. make[2]: Target `1ej0A/1ej0A-T0126-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ej0A/xxxx-1ej0A-T0126-local.pw.a2m.gz'. make[2]: Target `1ej0A/xxxx-1ej0A-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1ej0A/xxxx-1ej0A-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.57.1 3.57.1 make -k PRED=1atzA PRED2=1a A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 1atzA/T0126-1atzA-local.pw.a2m.gz 1atzA/1atzA-T0126-local.pw.a2m.gz \ 1atzA/T0126-1atzA-2track-local.pw.a2m.gz \ 1atzA/T0126-1atzA-2track-global.pw.a2m.gz \ 1atzA/T0126-1atzA-vit.pw.a2m.gz 1atzA/1atzA-T0126-vit.pw.a2m.gz \ 1atzA/T0126-1atzA-global.pw.a2m.gz 1atzA/1atzA-T0126-global.pw.a2m.gz \ 1atzA/1atzA-T0126-fssp-global.pw.a2m.gz \ 1atzA/xxxx-1atzA-T0126-local.pw.a2m.gz 1atzA/xxxx-1atzA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 1atzA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1atzA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1atzA/T0126-1atzA-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -67.121193 Database has 3 sequences with 536 residues. gzip -f 1atzA/T0126-1atzA-local.pw.a2m make[2]: `1atzA/1atzA-T0126-local.pw.a2m.gz' is up to date. make 1atzA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1atzA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1atzA/T0126-1atzA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1atzA/T0126-1atzA-2track-local.pw.a2m.gz] Error 1 make 1atzA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1atzA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1atzA/T0126-1atzA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [1atzA/T0126-1atzA-2track-global.pw.a2m.gz] Error 1 make 1atzA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1atzA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1atzA/T0126-1atzA-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -62.479172 Database has 3 sequences with 536 residues. gzip -f 1atzA/T0126-1atzA-vit.pw.a2m make[2]: `1atzA/1atzA-T0126-vit.pw.a2m.gz' is up to date. make 1atzA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `1atzA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 1atzA/T0126-1atzA-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1atzA/info/1atzA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -49.576679 Database has 3 sequences with 536 residues. gzip -f 1atzA/T0126-1atzA-global.pw.a2m make[2]: `1atzA/1atzA-T0126-global.pw.a2m.gz' is up to date. make[2]: `1atzA/1atzA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1atzA/xxxx-1atzA-T0126-local.pw.a2m.gz'. make[2]: Target `1atzA/xxxx-1atzA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1atzA/xxxx-1atzA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) echo 3.1.* 3.1.* make -k PRED=2tpsA PRED2=2t A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 2tpsA/T0126-2tpsA-local.pw.a2m.gz 2tpsA/2tpsA-T0126-local.pw.a2m.gz \ 2tpsA/T0126-2tpsA-2track-local.pw.a2m.gz \ 2tpsA/T0126-2tpsA-2track-global.pw.a2m.gz \ 2tpsA/T0126-2tpsA-vit.pw.a2m.gz 2tpsA/2tpsA-T0126-vit.pw.a2m.gz \ 2tpsA/T0126-2tpsA-global.pw.a2m.gz 2tpsA/2tpsA-T0126-global.pw.a2m.gz \ 2tpsA/2tpsA-T0126-fssp-global.pw.a2m.gz \ 2tpsA/xxxx-2tpsA-T0126-local.pw.a2m.gz 2tpsA/xxxx-2tpsA-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 2tpsA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2tpsA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2tpsA/T0126-2tpsA-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -66.775253 Database has 3 sequences with 616 residues. gzip -f 2tpsA/T0126-2tpsA-local.pw.a2m make[2]: `2tpsA/2tpsA-T0126-local.pw.a2m.gz' is up to date. make 2tpsA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2tpsA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2tpsA/T0126-2tpsA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [2tpsA/T0126-2tpsA-2track-local.pw.a2m.gz] Error 1 make 2tpsA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2tpsA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2tpsA/T0126-2tpsA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [2tpsA/T0126-2tpsA-2track-global.pw.a2m.gz] Error 1 make 2tpsA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2tpsA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2tpsA/T0126-2tpsA-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -62.012249 Database has 3 sequences with 616 residues. gzip -f 2tpsA/T0126-2tpsA-vit.pw.a2m make[2]: `2tpsA/2tpsA-T0126-vit.pw.a2m.gz' is up to date. make 2tpsA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2tpsA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2tpsA/T0126-2tpsA-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2t/2tpsA/info/2tpsA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -38.848991 Database has 3 sequences with 616 residues. gzip -f 2tpsA/T0126-2tpsA-global.pw.a2m make[2]: `2tpsA/2tpsA-T0126-global.pw.a2m.gz' is up to date. make[2]: `2tpsA/2tpsA-T0126-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2tpsA/xxxx-2tpsA-T0126-local.pw.a2m.gz'. make[2]: Target `2tpsA/xxxx-2tpsA-T0126-local.pw.a2m.gz' not remade because of errors. make[2]: Target `2tpsA/xxxx-2tpsA-T0126-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' make: [joints] Error 2 (ignored) make -k PRED=2myr PRED2=2m A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make -k \ 2myr/T0126-2myr-local.pw.a2m.gz 2myr/2myr-T0126-local.pw.a2m.gz \ 2myr/T0126-2myr-2track-local.pw.a2m.gz \ 2myr/T0126-2myr-2track-global.pw.a2m.gz \ 2myr/T0126-2myr-vit.pw.a2m.gz 2myr/2myr-T0126-vit.pw.a2m.gz \ 2myr/T0126-2myr-global.pw.a2m.gz 2myr/2myr-T0126-global.pw.a2m.gz \ 2myr/2myr-T0126-fssp-global.pw.a2m.gz \ 2myr/xxxx-2myr-T0126-local.pw.a2m.gz 2myr/xxxx-2myr-T0126-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' mkdir 2myr fixmode 2myr make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/T0126-2myr-local.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -69.552681 Database has 3 sequences with 1163 residues. gzip -f 2myr/T0126-2myr-local.pw.a2m make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/2myr-T0126-local.pw -i /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19790/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: -308.800629 Database has 3 sequences with 1163 residues. gzip -f 2myr/2myr-T0126-local.pw.a2m make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/T0126-2myr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq,/projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.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 T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [2myr/T0126-2myr-2track-local.pw.a2m.gz] Error 1 make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/T0126-2myr-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0126.remoter-t2k-w0.5.mod,T0126.remoter-t2k-2d.mod \ -db T0126.seq,T0126.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq,/projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.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. T0126.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/tmp.a2m T0126.remoter-t2k-2d.mod(1007): Reading track 1 model from MODEL -- Model from 2nd structure file T0126.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error: Couldn't open file T0126.remoter-t2k.2d.seq: No such file or directory make[2]: *** [2myr/T0126-2myr-2track-global.pw.a2m.gz] Error 1 make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/T0126-2myr-vit.pw \ -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -63.777020 Database has 3 sequences with 1163 residues. gzip -f 2myr/T0126-2myr-vit.pw.a2m make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/2myr-T0126-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19790/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: -304.595703 Database has 3 sequences with 1163 residues. gzip -f 2myr/2myr-T0126-vit.pw.a2m make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/T0126-2myr-global.pw -i T0126.remoter-t2k-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0126.remoter-t2k-w0.5.mod T0126.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22776/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: -10.953682 Database has 3 sequences with 1163 residues. gzip -f 2myr/T0126-2myr-global.pw.a2m make 2myr make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t126' make[3]: `2myr' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t126' /projects/compbio/bin/alpha.new/hmmscore 2myr/2myr-T0126-global.pw -i /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod -db T0126.seq -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2m/2myr/info/2myr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2m/2myr/nostruct-align/2myr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19790/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: -294.228363 Database has 3 sequences with 1163 residues. gzip -f 2myr/2myr-T0126-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2m/2myr/struct-align/2myr.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2m/2myr/struct-align/2myr.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18856 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18856/tmp -alignfile /projects/compbio/experiments/models.97/pdb/2m/2myr/struct-align/2myr.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/2m/2myr/struct-align/2myr.fssp.a2m.gz (113 sequences, 499 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18856/tmp.a2m. Dropping 31 (of 113) duplicate sequences with differing IDs Dropping 6 (of 113) sequences with > 80.0% id 76 sequences left after dropping 37 of 113 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18856/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18856/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-18856/tmp.a2m (76 sequences, 499 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18856/tmp.mod /projects/compbio/experiments/models.97/pdb/2m/2myr/struct-align/2myr.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18856 80.0% id 55 sequences left after dropping 1 of 56 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21644/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21644/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-21644/tmp.a2m (55 sequences, 279 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21644/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qumA/struct-align/1qumA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21644 80.0% id 1 sequences left after dropping 3 of 4 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16335/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16335/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-16335/tmp.a2m (1 sequences, 71 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16335/tmp.mod /projects/compbio/experiments/models.97/pdb/2b/2bb8/struct-align/2bb8.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16335