make -k PRED=2oneA PRED2=2o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make 2oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `2oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 2oneA/T0111-2oneA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0111.t2k-w0.5.mod,T0111.t2k-2d.mod \
 -db T0111.seq,T0111.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2oneA/T0111-2oneA-2track-local.pw.a2m
make 2oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `2oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 2oneA/T0111-2oneA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0111.t2k-w0.5.mod,T0111.t2k-2d.mod \
 -db T0111.seq,T0111.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride.seq,/projects/compbio/experiments/models.97/pdb/2o/2oneA/info/2oneA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2oneA/T0111-2oneA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
make -k PRED=1oneA PRED2=1o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
mkdir 1oneA
fixmode 1oneA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/T0111-1oneA-local.pw -i T0111.t2k-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/T0111-1oneA-local.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/1oneA-T0111-local.pw -i /projects/compbio/experiments/models.97/pdb/1o/1oneA/nostruct-align/1oneA.t99-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/1oneA-T0111-local.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/T0111-1oneA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0111.t2k-w0.5.mod,T0111.t2k-2d.mod \
 -db T0111.seq,T0111.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/T0111-1oneA-2track-local.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/T0111-1oneA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0111.t2k-w0.5.mod,T0111.t2k-2d.mod \
 -db T0111.seq,T0111.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/T0111-1oneA-2track-global.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/T0111-1oneA-vit.pw \
	-i T0111.t2k-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/T0111-1oneA-vit.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/1oneA-T0111-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1o/1oneA/nostruct-align/1oneA.t99-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/1oneA-T0111-vit.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/T0111-1oneA-global.pw -i T0111.t2k-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/T0111-1oneA-global.pw.a2m
make 1oneA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `1oneA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 1oneA/1oneA-T0111-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1oneA/nostruct-align/1oneA.t99-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1oneA/info/1oneA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1oneA/1oneA-T0111-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
make -k PRED=4enl  PRED2=4e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
mkdir 4enl
fixmode 4enl
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/T0111-4enl-local.pw -i T0111.t2k-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/T0111-4enl-local.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/4enl-T0111-local.pw -i /projects/compbio/experiments/models.97/pdb/4e/4enl/nostruct-align/4enl.t99-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/4enl-T0111-local.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/T0111-4enl-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0111.t2k-w0.5.mod,T0111.t2k-2d.mod \
 -db T0111.seq,T0111.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq,/projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/T0111-4enl-2track-local.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/T0111-4enl-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0111.t2k-w0.5.mod,T0111.t2k-2d.mod \
 -db T0111.seq,T0111.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq,/projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/T0111-4enl-2track-global.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/T0111-4enl-vit.pw \
	-i T0111.t2k-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/T0111-4enl-vit.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/4enl-T0111-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/4e/4enl/nostruct-align/4enl.t99-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/4enl-T0111-vit.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/T0111-4enl-global.pw -i T0111.t2k-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/T0111-4enl-global.pw.a2m
make 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/4enl-T0111-global.pw -i /projects/compbio/experiments/models.97/pdb/4e/4enl/nostruct-align/4enl.t99-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/4enl-T0111-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/4e/4enl/struct-align/4enl.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/4e/4enl/struct-align/4enl.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 4enl
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t111'
make[2]: `4enl' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'
/projects/compbio/bin/alpha.new/hmmscore 4enl/4enl-T0111-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/4e/4enl/struct-align/4enl.fssp-w0.5.mod -db T0111.seq -db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/4e/4enl/info/4enl.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 4enl/4enl-T0111-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t111'