make -k PRED=2tysA PRED2=2t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 2tysA
fixmode 2tysA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/T0118-2tysA-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/T0118-2tysA-local.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/2tysA-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/2t/2tysA/nostruct-align/2tysA.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/2tysA-T0118-local.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/T0118-2tysA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq,/projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/T0118-2tysA-2track-local.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/T0118-2tysA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq,/projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/T0118-2tysA-2track-global.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/T0118-2tysA-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/T0118-2tysA-vit.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/2tysA-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2t/2tysA/nostruct-align/2tysA.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/2tysA-T0118-vit.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/T0118-2tysA-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/T0118-2tysA-global.pw.a2m
make 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/2tysA-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/2t/2tysA/nostruct-align/2tysA.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/2tysA-T0118-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2t/2tysA/struct-align/2tysA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2t/2tysA/struct-align/2tysA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 2tysA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `2tysA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 2tysA/2tysA-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2t/2tysA/struct-align/2tysA.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2t/2tysA/info/2tysA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2tysA/2tysA-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1b78A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1b78A
fixmode 1b78A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0118-1b78A-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0118-1b78A-local.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/1b78A-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b78A/nostruct-align/1b78A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/1b78A-T0118-local.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0118-1b78A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0118-1b78A-2track-local.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0118-1b78A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0118-1b78A-2track-global.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0118-1b78A-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0118-1b78A-vit.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/1b78A-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1b78A/nostruct-align/1b78A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/1b78A-T0118-vit.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/T0118-1b78A-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/T0118-1b78A-global.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/1b78A-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b78A/nostruct-align/1b78A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/1b78A-T0118-global.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b78A/1b78A-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b78A/1b78A-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1anf  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1anf
fixmode 1anf
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/T0118-1anf-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/T0118-1anf-local.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/1anf-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1anf/nostruct-align/1anf.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/1anf-T0118-local.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/T0118-1anf-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/T0118-1anf-2track-local.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/T0118-1anf-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/T0118-1anf-2track-global.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/T0118-1anf-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/T0118-1anf-vit.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/1anf-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1anf/nostruct-align/1anf.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/1anf-T0118-vit.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/T0118-1anf-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/T0118-1anf-global.pw.a2m
make 1anf
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1anf' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1anf/1anf-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1anf/nostruct-align/1anf.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1anf/info/1anf.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1anf/1anf-T0118-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=4mbp  PRED2=4m joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 4mbp
fixmode 4mbp
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/T0118-4mbp-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/T0118-4mbp-local.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/4mbp-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/4m/4mbp/nostruct-align/4mbp.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/4mbp-T0118-local.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/T0118-4mbp-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq,/projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/T0118-4mbp-2track-local.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/T0118-4mbp-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq,/projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/T0118-4mbp-2track-global.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/T0118-4mbp-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/T0118-4mbp-vit.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/4mbp-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/4m/4mbp/nostruct-align/4mbp.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/4mbp-T0118-vit.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/T0118-4mbp-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/T0118-4mbp-global.pw.a2m
make 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/4mbp-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/4m/4mbp/nostruct-align/4mbp.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/4mbp-T0118-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/4m/4mbp/struct-align/4mbp.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/4m/4mbp/struct-align/4mbp.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 4mbp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `4mbp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 4mbp/4mbp-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/4m/4mbp/struct-align/4mbp.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4m/4mbp/info/4mbp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4mbp/4mbp-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1euu  PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1euu
fixmode 1euu
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/T0118-1euu-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/T0118-1euu-local.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/1euu-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1euu/nostruct-align/1euu.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/1euu-T0118-local.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/T0118-1euu-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/T0118-1euu-2track-local.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/T0118-1euu-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/T0118-1euu-2track-global.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/T0118-1euu-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/T0118-1euu-vit.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/1euu-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1e/1euu/nostruct-align/1euu.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/1euu-T0118-vit.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/T0118-1euu-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/T0118-1euu-global.pw.a2m
make 1euu
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1euu' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1euu/1euu-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1euu/nostruct-align/1euu.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1euu/info/1euu.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1euu/1euu-T0118-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1qo7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1qo7A
fixmode 1qo7A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/T0118-1qo7A-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/T0118-1qo7A-local.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/1qo7A-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qo7A/nostruct-align/1qo7A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/1qo7A-T0118-local.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/T0118-1qo7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/T0118-1qo7A-2track-local.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/T0118-1qo7A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/T0118-1qo7A-2track-global.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/T0118-1qo7A-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/T0118-1qo7A-vit.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/1qo7A-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qo7A/nostruct-align/1qo7A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/1qo7A-T0118-vit.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/T0118-1qo7A-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/T0118-1qo7A-global.pw.a2m
make 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/1qo7A-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qo7A/nostruct-align/1qo7A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/1qo7A-T0118-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qo7A/struct-align/1qo7A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qo7A/struct-align/1qo7A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1qo7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1qo7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1qo7A/1qo7A-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qo7A/struct-align/1qo7A.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qo7A/info/1qo7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qo7A/1qo7A-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=3grs  PRED2=3g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 3grs
fixmode 3grs
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/T0118-3grs-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/T0118-3grs-local.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/3grs-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/3g/3grs/nostruct-align/3grs.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/3grs-T0118-local.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/T0118-3grs-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq,/projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/T0118-3grs-2track-local.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/T0118-3grs-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq,/projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/T0118-3grs-2track-global.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/T0118-3grs-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/T0118-3grs-vit.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/3grs-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/3g/3grs/nostruct-align/3grs.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/3grs-T0118-vit.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/T0118-3grs-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/T0118-3grs-global.pw.a2m
make 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/3grs-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/3g/3grs/nostruct-align/3grs.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/3grs-T0118-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/3g/3grs/struct-align/3grs.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/3g/3grs/struct-align/3grs.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 3grs
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `3grs' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 3grs/3grs-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/3g/3grs/struct-align/3grs.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3g/3grs/info/3grs.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3grs/3grs-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1b12A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1b12A
fixmode 1b12A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/T0118-1b12A-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/T0118-1b12A-local.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/1b12A-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b12A/nostruct-align/1b12A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/1b12A-T0118-local.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/T0118-1b12A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/T0118-1b12A-2track-local.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/T0118-1b12A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/T0118-1b12A-2track-global.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/T0118-1b12A-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/T0118-1b12A-vit.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/1b12A-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1b12A/nostruct-align/1b12A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/1b12A-T0118-vit.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/T0118-1b12A-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/T0118-1b12A-global.pw.a2m
make 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/1b12A-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b12A/nostruct-align/1b12A.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/1b12A-T0118-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1b12A/struct-align/1b12A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1b12A/struct-align/1b12A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1b12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1b12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1b12A/1b12A-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b12A/struct-align/1b12A.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b12A/info/1b12A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b12A/1b12A-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1opr  PRED2=1o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1opr
fixmode 1opr
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/T0118-1opr-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/T0118-1opr-local.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/1opr-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/1opr-T0118-local.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/T0118-1opr-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/T0118-1opr-2track-local.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/T0118-1opr-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/T0118-1opr-2track-global.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/T0118-1opr-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/T0118-1opr-vit.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/1opr-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/1opr-T0118-vit.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/T0118-1opr-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/T0118-1opr-global.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/1opr-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/1opr-T0118-global.pw.a2m
make 1opr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1opr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1opr/1opr-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1opr/1opr-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
make -k PRED=1avqA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
mkdir 1avqA
fixmode 1avqA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/T0118-1avqA-local.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/T0118-1avqA-local.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/1avqA-T0118-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1avqA/nostruct-align/1avqA.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/1avqA-T0118-local.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/T0118-1avqA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/T0118-1avqA-2track-local.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/T0118-1avqA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0118.t2k-w0.5.mod,T0118.t2k-2d.mod \
 -db T0118.seq,T0118.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/T0118-1avqA-2track-global.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/T0118-1avqA-vit.pw \
	-i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/T0118-1avqA-vit.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/1avqA-T0118-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1avqA/nostruct-align/1avqA.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/1avqA-T0118-vit.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/T0118-1avqA-global.pw -i T0118.t2k-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/T0118-1avqA-global.pw.a2m
make 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/1avqA-T0118-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1avqA/nostruct-align/1avqA.t99-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/1avqA-T0118-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1avqA/struct-align/1avqA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1avqA/struct-align/1avqA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1avqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t118'
make[2]: `1avqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'
/projects/compbio/bin/alpha.new/hmmscore 1avqA/1avqA-T0118-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1avqA/struct-align/1avqA.fssp-w0.5.mod -db T0118.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avqA/info/1avqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1avqA/1avqA-T0118-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t118'