make -k PRED=2ohxA PRED2=2o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0087-2ohxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2ohxA/T0087-2ohxA-2track-local.pw.a2m
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2ohxA/T0087-2ohxA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2ohxA/T0087-2ohxA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1pjr PRED2=1p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1pjr/T0087-1pjr-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1pjr/T0087-1pjr-2track-local.pw.a2m
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1pjr/T0087-1pjr-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq,/projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1pjr/T0087-1pjr-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1tbgE PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tbgE/T0087-1tbgE-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tbgE/T0087-1tbgE-2track-local.pw.a2m
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tbgE/T0087-1tbgE-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tbgE/T0087-1tbgE-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1qhgB PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qhgB/T0087-1qhgB-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qhgB/T0087-1qhgB-2track-local.pw.a2m
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qhgB/T0087-1qhgB-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qhgB/T0087-1qhgB-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=2yhx  PRED2=2y joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 2yhx
fixmode 2yhx
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/T0087-2yhx-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/T0087-2yhx-local.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/2yhx-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/2y/2yhx/nostruct-align/2yhx.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/2yhx-T0087-local.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/T0087-2yhx-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq,/projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/T0087-2yhx-2track-local.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/T0087-2yhx-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq,/projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/T0087-2yhx-2track-global.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/T0087-2yhx-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/T0087-2yhx-vit.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/2yhx-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2y/2yhx/nostruct-align/2yhx.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/2yhx-T0087-vit.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/T0087-2yhx-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/T0087-2yhx-global.pw.a2m
make 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/2yhx-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/2y/2yhx/nostruct-align/2yhx.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/2yhx-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2y/2yhx/struct-align/2yhx.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2y/2yhx/struct-align/2yhx.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 2yhx
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2yhx' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 2yhx/2yhx-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2y/2yhx/struct-align/2yhx.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2y/2yhx/info/2yhx.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2yhx/2yhx-T0087-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1tgoA PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1tgoA
fixmode 1tgoA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0087-1tgoA-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0087-1tgoA-local.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/nostruct-align/1tgoA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0087-local.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0087-1tgoA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0087-1tgoA-2track-local.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0087-1tgoA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0087-1tgoA-2track-global.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0087-1tgoA-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0087-1tgoA-vit.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/nostruct-align/1tgoA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0087-vit.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/T0087-1tgoA-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/T0087-1tgoA-global.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/nostruct-align/1tgoA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0087-global.pw.a2m
make 1tgoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tgoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1tgoA/1tgoA-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tgoA/struct-align/1tgoA.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tgoA/info/1tgoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1tgoA/1tgoA-T0087-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1mrj  PRED2=1m joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1mrj
fixmode 1mrj
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/T0087-1mrj-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/T0087-1mrj-local.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/1mrj-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1m/1mrj/nostruct-align/1mrj.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/1mrj-T0087-local.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/T0087-1mrj-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq,/projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/T0087-1mrj-2track-local.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/T0087-1mrj-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq,/projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/T0087-1mrj-2track-global.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/T0087-1mrj-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/T0087-1mrj-vit.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/1mrj-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1m/1mrj/nostruct-align/1mrj.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/1mrj-T0087-vit.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/T0087-1mrj-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/T0087-1mrj-global.pw.a2m
make 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/1mrj-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1m/1mrj/nostruct-align/1mrj.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/1mrj-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1m/1mrj/struct-align/1mrj.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1m/1mrj/struct-align/1mrj.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1mrj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1mrj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1mrj/1mrj-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1m/1mrj/struct-align/1mrj.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mrj/info/1mrj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1mrj/1mrj-T0087-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1qh8A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1qh8A
fixmode 1qh8A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/T0087-1qh8A-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/T0087-1qh8A-local.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/1qh8A-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qh8A/nostruct-align/1qh8A.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/1qh8A-T0087-local.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/T0087-1qh8A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/T0087-1qh8A-2track-local.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/T0087-1qh8A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/T0087-1qh8A-2track-global.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/T0087-1qh8A-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/T0087-1qh8A-vit.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/1qh8A-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qh8A/nostruct-align/1qh8A.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/1qh8A-T0087-vit.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/T0087-1qh8A-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/T0087-1qh8A-global.pw.a2m
make 1qh8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qh8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1qh8A/1qh8A-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qh8A/nostruct-align/1qh8A.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh8A/info/1qh8A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1qh8A/1qh8A-T0087-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1bykA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1bykA
fixmode 1bykA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/T0087-1bykA-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/T0087-1bykA-local.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/1bykA-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bykA/nostruct-align/1bykA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/1bykA-T0087-local.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/T0087-1bykA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/T0087-1bykA-2track-local.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/T0087-1bykA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/T0087-1bykA-2track-global.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/T0087-1bykA-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/T0087-1bykA-vit.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/1bykA-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bykA/nostruct-align/1bykA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/1bykA-T0087-vit.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/T0087-1bykA-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/T0087-1bykA-global.pw.a2m
make 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/1bykA-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bykA/nostruct-align/1bykA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/1bykA-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bykA/struct-align/1bykA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bykA/struct-align/1bykA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1bykA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1bykA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1bykA/1bykA-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bykA/struct-align/1bykA.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bykA/info/1bykA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bykA/1bykA-T0087-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make -k PRED=1pjr PRED2=1p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pjr/xxxx-1pjr-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1tbgE PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tbgE/xxxx-1tbgE-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1qhgB PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t99-w0.5.mod', needed by `1qhgB/1qhgB-T0087-local.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qhgB/struct-align/1qhgB.fssp-w0.5.mod', needed by `1qhgB/1qhgB-T0087-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhgB/xxxx-1qhgB-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=2yhx  PRED2=2y joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2yhx/xxxx-2yhx-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1tgoA PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tgoA/xxxx-1tgoA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1mrj  PRED2=1m joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1mrj/xxxx-1mrj-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1qh8A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh8A/struct-align/1qh8A.fssp-w0.5.mod', needed by `1qh8A/1qh8A-T0087-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh8A/xxxx-1qh8A-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1bykA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bykA/xxxx-1bykA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1cby  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cby/xxxx-1cby-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1b8wA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8wA/xxxx-1b8wA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1uroA PRED2=1u joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1uroA/xxxx-1uroA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
echo 4.72.1
4.72.1
make -k PRED=1lvl PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1lvl
fixmode 1lvl
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/T0087-1lvl-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -95.251190
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/T0087-1lvl-local.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/1lvl-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2619/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:        -221.200211
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/1lvl-T0087-local.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/T0087-1lvl-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -96.693909
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/T0087-1lvl-2track-local.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/T0087-1lvl-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -86.373016
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/T0087-1lvl-2track-global.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/T0087-1lvl-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -89.848183
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/T0087-1lvl-vit.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/1lvl-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2619/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:        -214.862564
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/1lvl-T0087-vit.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/T0087-1lvl-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -81.383331
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/T0087-1lvl-global.pw.a2m
make 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/1lvl-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lvl/nostruct-align/1lvl.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2619/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:        -218.291992
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/1lvl-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9938


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9938/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.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/1l/1lvl/struct-align/1lvl.fssp.a2m.gz (34 sequences, 458 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9938/tmp.a2m.
Dropping 7 (of 34) duplicate sequences with differing IDs
Dropping 5 (of 34) sequences with > 80.0% id
22 sequences left after dropping 12 of 34 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9938/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9938/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-9938/tmp.a2m (22 sequences, 458 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9938/tmp.mod /projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9938 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1lvl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1lvl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1lvl/1lvl-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lvl/info/1lvl.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lvl/struct-align/1lvl.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9938/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:        -252.761658
Database has 3 sequences with 1226 residues.
gzip -f 1lvl/1lvl-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lvl/xxxx-1lvl-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=3ladA PRED2=3l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 3ladA
fixmode 3ladA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/T0087-3ladA-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -95.280998
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/T0087-3ladA-local.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/3ladA-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27873/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:        -231.668381
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/3ladA-T0087-local.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/T0087-3ladA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq,/projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -96.520668
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/T0087-3ladA-2track-local.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/T0087-3ladA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq,/projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -86.848671
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/T0087-3ladA-2track-global.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/T0087-3ladA-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -90.370026
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/T0087-3ladA-vit.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/3ladA-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27873/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:        -227.112015
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/3ladA-T0087-vit.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/T0087-3ladA-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -82.479324
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/T0087-3ladA-global.pw.a2m
make 3ladA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `3ladA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 3ladA/3ladA-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/3l/3ladA/info/3ladA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/3l/3ladA/nostruct-align/3ladA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27873/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:        -225.714981
Database has 3 sequences with 1258 residues.
gzip -f 3ladA/3ladA-T0087-global.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3l/3ladA/struct-align/3ladA.fssp-w0.5.mod', needed by `3ladA/3ladA-T0087-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3ladA/xxxx-3ladA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
echo 1.3.1
1.3.1
make -k PRED=1c53 PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1c53
fixmode 1c53
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/T0087-1c53-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -94.248840
Database has 3 sequences with 468 residues.
gzip -f 1c53/T0087-1c53-local.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/1c53-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2769/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:        -40.624855
Database has 3 sequences with 468 residues.
gzip -f 1c53/1c53-T0087-local.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/T0087-1c53-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -93.296844
Database has 3 sequences with 468 residues.
gzip -f 1c53/T0087-1c53-2track-local.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/T0087-1c53-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -68.459671
Database has 3 sequences with 468 residues.
gzip -f 1c53/T0087-1c53-2track-global.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/T0087-1c53-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -89.525177
Database has 3 sequences with 468 residues.
gzip -f 1c53/T0087-1c53-vit.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/1c53-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2769/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:        -37.278847
Database has 3 sequences with 468 residues.
gzip -f 1c53/1c53-T0087-vit.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/T0087-1c53-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -67.841995
Database has 3 sequences with 468 residues.
gzip -f 1c53/T0087-1c53-global.pw.a2m
make 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/1c53-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c53/nostruct-align/1c53.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2769/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:        -40.014671
Database has 3 sequences with 468 residues.
gzip -f 1c53/1c53-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25852


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25852/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.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/1c/1c53/struct-align/1c53.fssp.a2m.gz (5 sequences, 79 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25852/tmp.a2m.
Dropping 1 (of 5) sequences with > 80.0% id
4 sequences left after dropping 1 of 5 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25852/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25852/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-25852/tmp.a2m (4 sequences, 79 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25852/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25852 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1c53
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1c53' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1c53/1c53-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c53/info/1c53.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c53/struct-align/1c53.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25852/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:        -57.398327
Database has 3 sequences with 468 residues.
gzip -f 1c53/1c53-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c53/xxxx-1c53-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
echo 11.7.1
11.7.1
make -k PRED=4hb1 PRED2=4h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 4hb1
fixmode 4hb1
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/T0087-4hb1-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -94.135704
Database has 3 sequences with 462 residues.
gzip -f 4hb1/T0087-4hb1-local.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/4hb1-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9049/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:        -34.306705
Database has 3 sequences with 462 residues.
gzip -f 4hb1/4hb1-T0087-local.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/T0087-4hb1-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq,/projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -94.912041
Database has 3 sequences with 462 residues.
gzip -f 4hb1/T0087-4hb1-2track-local.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/T0087-4hb1-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq,/projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -68.486000
Database has 3 sequences with 462 residues.
gzip -f 4hb1/T0087-4hb1-2track-global.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/T0087-4hb1-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -89.577049
Database has 3 sequences with 462 residues.
gzip -f 4hb1/T0087-4hb1-vit.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/4hb1-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9049/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:        -30.959707
Database has 3 sequences with 462 residues.
gzip -f 4hb1/4hb1-T0087-vit.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/T0087-4hb1-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -66.513336
Database has 3 sequences with 462 residues.
gzip -f 4hb1/T0087-4hb1-global.pw.a2m
make 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/4hb1-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/4h/4hb1/nostruct-align/4hb1.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9049/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:        -27.183661
Database has 3 sequences with 462 residues.
gzip -f 4hb1/4hb1-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23337


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23337/tmp -alignfile /projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.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/4h/4hb1/struct-align/4hb1.fssp.a2m.gz (60 sequences, 44 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23337/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23337/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23337/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-23337/tmp.a2m (60 sequences, 44 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23337/tmp.mod /projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23337 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 4hb1
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `4hb1' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 4hb1/4hb1-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4h/4hb1/info/4hb1.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/4h/4hb1/struct-align/4hb1.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23337/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:        -13.357669
Database has 3 sequences with 462 residues.
gzip -f 4hb1/4hb1-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `4hb1/xxxx-4hb1-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
echo 2.38.4
2.38.4
make -k PRED=1sro PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1sro
fixmode 1sro
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/T0087-1sro-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -94.714653
Database has 3 sequences with 462 residues.
gzip -f 1sro/T0087-1sro-local.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/1sro-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27024/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:        -48.920319
Database has 3 sequences with 462 residues.
gzip -f 1sro/1sro-T0087-local.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/T0087-1sro-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -92.885651
Database has 3 sequences with 462 residues.
gzip -f 1sro/T0087-1sro-2track-local.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/T0087-1sro-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -66.313339
Database has 3 sequences with 462 residues.
gzip -f 1sro/T0087-1sro-2track-global.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/T0087-1sro-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -90.684990
Database has 3 sequences with 462 residues.
gzip -f 1sro/T0087-1sro-vit.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/1sro-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27024/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:        -44.895313
Database has 3 sequences with 462 residues.
gzip -f 1sro/1sro-T0087-vit.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/T0087-1sro-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -68.437340
Database has 3 sequences with 462 residues.
gzip -f 1sro/T0087-1sro-global.pw.a2m
make 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/1sro-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sro/nostruct-align/1sro.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27024/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:        -48.367992
Database has 3 sequences with 462 residues.
gzip -f 1sro/1sro-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29612


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29612/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.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/1s/1sro/struct-align/1sro.fssp.a2m.gz (1 sequences, 76 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29612/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29612/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29612/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-29612/tmp.a2m (1 sequences, 76 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29612/tmp.mod /projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29612 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1sro
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1sro' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1sro/1sro-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sro/info/1sro.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sro/struct-align/1sro.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29612/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:        -54.119003
Database has 3 sequences with 462 residues.
gzip -f 1sro/1sro-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sro/xxxx-1sro-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1quqA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1quqA
fixmode 1quqA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/T0087-1quqA-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -94.553932
Database has 3 sequences with 560 residues.
gzip -f 1quqA/T0087-1quqA-local.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/1quqA-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21787/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:        -86.561256
Database has 3 sequences with 560 residues.
gzip -f 1quqA/1quqA-T0087-local.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/T0087-1quqA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -94.326607
Database has 3 sequences with 560 residues.
gzip -f 1quqA/T0087-1quqA-2track-local.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/T0087-1quqA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -71.410660
Database has 3 sequences with 560 residues.
gzip -f 1quqA/T0087-1quqA-2track-global.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/T0087-1quqA-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -90.628273
Database has 3 sequences with 560 residues.
gzip -f 1quqA/T0087-1quqA-vit.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/1quqA-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21787/tmp.a2m
SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -83.495949
Database has 3 sequences with 560 residues.
gzip -f 1quqA/1quqA-T0087-vit.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/T0087-1quqA-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -76.316345
Database has 3 sequences with 560 residues.
gzip -f 1quqA/T0087-1quqA-global.pw.a2m
make 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/1quqA-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1quqA/nostruct-align/1quqA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21787/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:        -82.425331
Database has 3 sequences with 560 residues.
gzip -f 1quqA/1quqA-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20065


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20065/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.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/1q/1quqA/struct-align/1quqA.fssp.a2m.gz (11 sequences, 121 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20065/tmp.a2m.
Dropping 1 (of 11) sequences with > 80.0% id
10 sequences left after dropping 1 of 11 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20065/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20065/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-20065/tmp.a2m (10 sequences, 121 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20065/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20065 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1quqA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1quqA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1quqA/1quqA-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quqA/info/1quqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1quqA/struct-align/1quqA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20065/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:        -70.168671
Database has 3 sequences with 560 residues.
gzip -f 1quqA/1quqA-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1quqA/xxxx-1quqA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
echo 3.88.1
3.88.1
make -k PRED=1gca  PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 1gca
fixmode 1gca
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/T0087-1gca-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -94.989586
Database has 3 sequences with 928 residues.
gzip -f 1gca/T0087-1gca-local.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/1gca-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23956/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:        -160.301254
Database has 3 sequences with 928 residues.
gzip -f 1gca/1gca-T0087-local.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/T0087-1gca-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -102.608910
Database has 3 sequences with 928 residues.
gzip -f 1gca/T0087-1gca-2track-local.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/T0087-1gca-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -93.946999
Database has 3 sequences with 928 residues.
gzip -f 1gca/T0087-1gca-2track-global.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/T0087-1gca-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -89.518585
Database has 3 sequences with 928 residues.
gzip -f 1gca/T0087-1gca-vit.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/1gca-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23956/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:        -157.440262
Database has 3 sequences with 928 residues.
gzip -f 1gca/1gca-T0087-vit.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/T0087-1gca-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -81.146019
Database has 3 sequences with 928 residues.
gzip -f 1gca/T0087-1gca-global.pw.a2m
make 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/1gca-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gca/nostruct-align/1gca.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23956/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:        -155.809662
Database has 3 sequences with 928 residues.
gzip -f 1gca/1gca-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29756


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29756/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.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/1g/1gca/struct-align/1gca.fssp.a2m.gz (70 sequences, 309 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29756/tmp.a2m.
Dropping 2 (of 70) duplicate sequences with differing IDs
Dropping 2 (of 70) sequences with > 80.0% id
66 sequences left after dropping 4 of 70 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29756/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29756/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-29756/tmp.a2m (66 sequences, 309 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29756/tmp.mod /projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29756 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1gca
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1gca' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 1gca/1gca-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gca/info/1gca.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gca/struct-align/1gca.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29756/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:        -122.376648
Database has 3 sequences with 928 residues.
gzip -f 1gca/1gca-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gca/xxxx-1gca-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=8abp  PRED2=8a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
mkdir 8abp
fixmode 8abp
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/T0087-8abp-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -95.866180
Database has 3 sequences with 921 residues.
gzip -f 8abp/T0087-8abp-local.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/8abp-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5394/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:        -147.998856
Database has 3 sequences with 921 residues.
gzip -f 8abp/8abp-T0087-local.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/T0087-8abp-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq,/projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.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
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.374840
Database has 3 sequences with 921 residues.
gzip -f 8abp/T0087-8abp-2track-local.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/T0087-8abp-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0087.t2k-w0.5.mod,T0087.t2k-2d.mod \
 -db T0087.seq,T0087.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq,/projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.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.
T0087.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file T0087.t2k.a2m.gz
T0087.t2k-2d.mod(1889):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -99.702667
Database has 3 sequences with 921 residues.
gzip -f 8abp/T0087-8abp-2track-global.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/T0087-8abp-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -90.574165
Database has 3 sequences with 921 residues.
gzip -f 8abp/T0087-8abp-vit.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/8abp-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5394/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:        -145.272522
Database has 3 sequences with 921 residues.
gzip -f 8abp/8abp-T0087-vit.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/T0087-8abp-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
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:        -84.082336
Database has 3 sequences with 921 residues.
gzip -f 8abp/T0087-8abp-global.pw.a2m
make 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/8abp-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/8a/8abp/nostruct-align/8abp.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5394/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:        -142.155670
Database has 3 sequences with 921 residues.
gzip -f 8abp/8abp-T0087-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31016


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31016/tmp -alignfile /projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.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/8a/8abp/struct-align/8abp.fssp.a2m.gz (51 sequences, 305 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31016/tmp.a2m.
Dropping 5 (of 51) duplicate sequences with differing IDs
Dropping 3 (of 51) sequences with > 80.0% id
43 sequences left after dropping 8 of 51 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31016/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31016/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-31016/tmp.a2m (43 sequences, 305 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31016/tmp.mod /projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31016 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 8abp
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `8abp' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
/projects/compbio/bin/alpha.new/hmmscore 8abp/8abp-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/8a/8abp/info/8abp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/8a/8abp/struct-align/8abp.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31016/tmp.a2m
SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -135.689667
Database has 3 sequences with 921 residues.
gzip -f 8abp/8abp-T0087-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `8abp/xxxx-8abp-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
echo 3.31.1	 (also 2.41.3)
/bin/sh: syntax error at line 1: `(' unexpected
make: *** [joints] Error 2