make -k PRED=1cqxA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make 1cqxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1cqxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1cqxA/T0119-1cqxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1cqxA/T0119-1cqxA-2track-local.pw.a2m make 1cqxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1cqxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1cqxA/T0119-1cqxA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cqxA/info/1cqxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1cqxA/T0119-1cqxA-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make -k PRED=1qfjA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' mkdir 1qfjA fixmode 1qfjA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/T0119-1qfjA-local.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/T0119-1qfjA-local.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/1qfjA-T0119-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qfjA/nostruct-align/1qfjA.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/1qfjA-T0119-local.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/T0119-1qfjA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/T0119-1qfjA-2track-local.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/T0119-1qfjA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/T0119-1qfjA-2track-global.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/T0119-1qfjA-vit.pw \ -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/T0119-1qfjA-vit.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/1qfjA-T0119-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1q/1qfjA/nostruct-align/1qfjA.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/1qfjA-T0119-vit.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/T0119-1qfjA-global.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/T0119-1qfjA-global.pw.a2m make 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/1qfjA-T0119-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qfjA/nostruct-align/1qfjA.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/1qfjA-T0119-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qfjA/struct-align/1qfjA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qfjA/struct-align/1qfjA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1qfjA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qfjA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qfjA/1qfjA-T0119-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qfjA/struct-align/1qfjA.fssp-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qfjA/info/1qfjA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qfjA/1qfjA-T0119-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make -k PRED=1ndh PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' mkdir 1ndh fixmode 1ndh make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/T0119-1ndh-local.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/T0119-1ndh-local.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/1ndh-T0119-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ndh/nostruct-align/1ndh.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/1ndh-T0119-local.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/T0119-1ndh-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/T0119-1ndh-2track-local.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/T0119-1ndh-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/T0119-1ndh-2track-global.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/T0119-1ndh-vit.pw \ -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/T0119-1ndh-vit.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/1ndh-T0119-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1ndh/nostruct-align/1ndh.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/1ndh-T0119-vit.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/T0119-1ndh-global.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/T0119-1ndh-global.pw.a2m make 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/1ndh-T0119-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ndh/nostruct-align/1ndh.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/1ndh-T0119-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1ndh/struct-align/1ndh.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1ndh/struct-align/1ndh.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1ndh make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndh' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndh/1ndh-T0119-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ndh/struct-align/1ndh.fssp-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndh/info/1ndh.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1ndh/1ndh-T0119-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make -k PRED=1awd PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make 1awd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1awd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1awd/T0119-1awd-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1awd/T0119-1awd-2track-local.pw.a2m make 1awd make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1awd' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1awd/T0119-1awd-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1awd/info/1awd.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1awd/T0119-1awd-2track-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make -k PRED=1qt9A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' mkdir 1qt9A fixmode 1qt9A make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/T0119-1qt9A-local.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/T0119-1qt9A-local.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/1qt9A-T0119-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qt9A/nostruct-align/1qt9A.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/1qt9A-T0119-local.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/T0119-1qt9A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/T0119-1qt9A-2track-local.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/T0119-1qt9A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/T0119-1qt9A-2track-global.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/T0119-1qt9A-vit.pw \ -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/T0119-1qt9A-vit.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/1qt9A-T0119-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1q/1qt9A/nostruct-align/1qt9A.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/1qt9A-T0119-vit.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/T0119-1qt9A-global.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/T0119-1qt9A-global.pw.a2m make 1qt9A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1qt9A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1qt9A/1qt9A-T0119-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qt9A/nostruct-align/1qt9A.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qt9A/info/1qt9A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1qt9A/1qt9A-T0119-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make -k PRED=1cqxA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cqxA/xxxx-1cqxA-T0119-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make: [joints] Error 2 (ignored) make -k PRED=1qfjA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfjA/xxxx-1qfjA-T0119-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make: [joints] Error 2 (ignored) make -k PRED=1ndh PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ndh/xxxx-1ndh-T0119-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make: [joints] Error 2 (ignored) make -k PRED=1awd PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1awd/xxxx-1awd-T0119-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make: [joints] Error 2 (ignored) make -k PRED=1qt9A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qt9A/struct-align/1qt9A.fssp-w0.5.mod', needed by `1qt9A/1qt9A-T0119-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qt9A/xxxx-1qt9A-T0119-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' make: [joints] Error 2 (ignored) make -k PRED=1ndoA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' mkdir 1ndoA fixmode 1ndoA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/T0119-1ndoA-local.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0119.t2k-w0.5.mod T0119.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-7253/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: -90.549828 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/T0119-1ndoA-local.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/1ndoA-T0119-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29853/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: -248.807114 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/1ndoA-T0119-local.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/T0119-1ndoA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.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 T0119.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-7253/tmp.a2m T0119.t2k-2d.mod(2057): Reading track 1 model from MODEL -- Model from 2nd structure file T0119.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -102.449440 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/T0119-1ndoA-2track-local.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/T0119-1ndoA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0119.t2k-w0.5.mod,T0119.t2k-2d.mod \ -db T0119.seq,T0119.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.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. T0119.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-7253/tmp.a2m T0119.t2k-2d.mod(2057): Reading track 1 model from MODEL -- Model from 2nd structure file T0119.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -89.548004 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/T0119-1ndoA-2track-global.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/T0119-1ndoA-vit.pw \ -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0119.t2k-w0.5.mod T0119.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-7253/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: -85.601799 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/T0119-1ndoA-vit.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/1ndoA-T0119-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29853/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: -244.392136 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/1ndoA-T0119-vit.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/T0119-1ndoA-global.pw -i T0119.t2k-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0119.t2k-w0.5.mod T0119.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-7253/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: -78.316025 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/T0119-1ndoA-global.pw.a2m make 1ndoA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t119' make[2]: `1ndoA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t119' /projects/compbio/bin/alpha.new/hmmscore 1ndoA/1ndoA-T0119-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod -db T0119.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ndoA/info/1ndoA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ndoA/nostruct-align/1ndoA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29853/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: -243.778336 Database has 3 sequences with 1234 residues. gzip -f 1ndoA/1ndoA-T0119-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1ndoA/struct-align/1ndoA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1ndoA/struct-align/1ndoA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9420 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9420/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1n/1ndoA/struct-align/1ndoA.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/1n/1ndoA/struct-align/1ndoA.fssp.a2m.gz (4 sequences, 447 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9420/tmp.a2m. Dropping 1 (of 4) duplicate sequences with differing IDs Dropping 1 (of 4) sequences with > 80.0% id 2 sequences left after dropping 2 of 4 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9420/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9420/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-9420/tmp.a2m (2 sequences, 447 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9420/tmp.mod /projects/compbio/experiments/models.97/pdb/1n/1ndoA/struct-align/1ndoA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9420