make -k PRED=1qhiA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make 1qhiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `1qhiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 1qhiA/T0117-1qhiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qhiA/T0117-1qhiA-2track-local.pw.a2m
make 1qhiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `1qhiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 1qhiA/T0117-1qhiA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qhiA/T0117-1qhiA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
make -k PRED=3vtk  PRED2=3v joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make 3vtk
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3vtk' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3vtk/T0117-3vtk-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3vtk/T0117-3vtk-2track-local.pw.a2m
make 3vtk
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3vtk' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3vtk/T0117-3vtk-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3vtk/T0117-3vtk-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
make -k PRED=1kimA PRED2=1k joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make 1kimA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `1kimA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 1kimA/T0117-1kimA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kimA/T0117-1kimA-2track-local.pw.a2m
make 1kimA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `1kimA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 1kimA/T0117-1kimA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kimA/info/1kimA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1kimA/T0117-1kimA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
make -k PRED=5tmpA PRED2=5t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
mkdir 5tmpA
fixmode 5tmpA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/T0117-5tmpA-local.pw -i T0117.t2k-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/T0117-5tmpA-local.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/5tmpA-T0117-local.pw -i /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/5tmpA-T0117-local.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/T0117-5tmpA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/T0117-5tmpA-2track-local.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/T0117-5tmpA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/T0117-5tmpA-2track-global.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/T0117-5tmpA-vit.pw \
	-i T0117.t2k-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/T0117-5tmpA-vit.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/5tmpA-T0117-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/5tmpA-T0117-vit.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/T0117-5tmpA-global.pw -i T0117.t2k-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/T0117-5tmpA-global.pw.a2m
make 5tmpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `5tmpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 5tmpA/5tmpA-T0117-global.pw -i /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 5tmpA/5tmpA-T0117-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
make -k PRED=3tmkA PRED2=3t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
mkdir 3tmkA
fixmode 3tmkA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/T0117-3tmkA-local.pw -i T0117.t2k-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/T0117-3tmkA-local.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/3tmkA-T0117-local.pw -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/3tmkA-T0117-local.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/T0117-3tmkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/T0117-3tmkA-2track-local.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/T0117-3tmkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0117.t2k-w0.5.mod,T0117.t2k-2d.mod \
 -db T0117.seq,T0117.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/T0117-3tmkA-2track-global.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/T0117-3tmkA-vit.pw \
	-i T0117.t2k-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/T0117-3tmkA-vit.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/3tmkA-T0117-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/3tmkA-T0117-vit.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/T0117-3tmkA-global.pw -i T0117.t2k-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/T0117-3tmkA-global.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/3tmkA-T0117-global.pw -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/3tmkA-T0117-global.pw.a2m
make 3tmkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t117'
make[2]: `3tmkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'
/projects/compbio/bin/alpha.new/hmmscore 3tmkA/3tmkA-T0117-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp-w0.5.mod -db T0117.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 3tmkA/3tmkA-T0117-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t117'