make -k PRED=1do0A  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
mkdir 1do0A
fixmode 1do0A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0127-1do0A-local.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -135.409149
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/T0127-1do0A-local.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/1do0A-T0127-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17502/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:        -196.974792
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/1do0A-T0127-local.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0127-1do0A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.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
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -143.183136
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/T0127-1do0A-2track-local.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0127-1do0A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.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.
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -142.529663
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/T0127-1do0A-2track-global.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0127-1do0A-vit.pw \
	-i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -126.741463
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/T0127-1do0A-vit.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/1do0A-T0127-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17502/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:        -190.884781
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/1do0A-T0127-vit.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0127-1do0A-global.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -131.652664
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/T0127-1do0A-global.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/1do0A-T0127-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1do0A/nostruct-align/1do0A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17502/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:        -195.650681
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/1do0A-T0127-global.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/1do0A-T0127-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1do0A/struct-align/1do0A.fssp-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1do0A/struct-align/1do0A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1do0A/struct-align/1do0A.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-30390/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:        -333.126343
Database has 3 sequences with 1198 residues.
gzip -f 1do0A/1do0A-T0127-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1do0A/xxxx-1do0A-T0127-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
make: [joints] Error 2 (ignored)
make -k PRED=1a5t   PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
mkdir 1a5t
fixmode 1a5t
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/T0127-1a5t-local.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -106.832733
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/T0127-1a5t-local.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/1a5t-T0127-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24553/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:        -150.227066
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/1a5t-T0127-local.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/T0127-1a5t-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.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
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -123.865395
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/T0127-1a5t-2track-local.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/T0127-1a5t-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.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.
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -119.581657
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/T0127-1a5t-2track-global.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/T0127-1a5t-vit.pw \
	-i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -98.370735
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/T0127-1a5t-vit.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/1a5t-T0127-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24553/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:        -145.574722
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/1a5t-T0127-vit.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/T0127-1a5t-global.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -97.668999
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/T0127-1a5t-global.pw.a2m
make 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/1a5t-T0127-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a5t/nostruct-align/1a5t.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24553/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:        -147.637665
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/1a5t-T0127-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20051


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20051/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.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/1a/1a5t/struct-align/1a5t.fssp.a2m.gz (8 sequences, 323 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20051/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20051/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20051/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-20051/tmp.a2m (8 sequences, 323 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20051/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20051 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1a5t
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1a5t' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1a5t/1a5t-T0127-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.fssp-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a5t/info/1a5t.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a5t/struct-align/1a5t.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20051/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:        -224.664352
Database has 3 sequences with 1008 residues.
gzip -f 1a5t/1a5t-T0127-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a5t/xxxx-1a5t-T0127-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
make: [joints] Error 2 (ignored)
make -k PRED=1d2nA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
mkdir 1d2nA
fixmode 1d2nA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/T0127-1d2nA-local.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -100.827667
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/T0127-1d2nA-local.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/1d2nA-T0127-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16894/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:        -121.042992
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/1d2nA-T0127-local.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/T0127-1d2nA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.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
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -107.770477
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/T0127-1d2nA-2track-local.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/T0127-1d2nA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.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.
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.218170
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/T0127-1d2nA-2track-global.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/T0127-1d2nA-vit.pw \
	-i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -93.134987
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/T0127-1d2nA-vit.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/1d2nA-T0127-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16894/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:        -114.509308
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/1d2nA-T0127-vit.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/T0127-1d2nA-global.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -93.633339
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/T0127-1d2nA-global.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/1d2nA-T0127-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d2nA/nostruct-align/1d2nA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16894/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:        -118.479668
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/1d2nA-T0127-global.pw.a2m
make 1d2nA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `1d2nA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 1d2nA/1d2nA-T0127-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d2nA/struct-align/1d2nA.fssp-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d2nA/info/1d2nA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d2nA/struct-align/1d2nA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d2nA/struct-align/1d2nA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25339/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:        -155.629333
Database has 3 sequences with 868 residues.
gzip -f 1d2nA/1d2nA-T0127-fssp-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2nA/xxxx-1d2nA-T0127-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
make: [joints] Error 2 (ignored)
make -k PRED=2shkA  PRED2=2s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
mkdir 2shkA
fixmode 2shkA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0127-2shkA-local.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -98.221062
Database has 3 sequences with 681 residues.
gzip -f 2shkA/T0127-2shkA-local.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/2shkA-T0127-local.pw -i /projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17812/tmp.a2m
SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -85.949730
Database has 3 sequences with 681 residues.
gzip -f 2shkA/2shkA-T0127-local.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0127-2shkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.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
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -98.100067
Database has 3 sequences with 681 residues.
gzip -f 2shkA/T0127-2shkA-2track-local.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0127-2shkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0127.t2k-w0.5.mod,T0127.t2k-2d.mod \
 -db T0127.seq,T0127.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq,/projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.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.
T0127.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/tmp.a2m
T0127.t2k-2d.mod(2129):  Reading track 1 model from MODEL -- Model from 2nd structure file T0127.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -92.519997
Database has 3 sequences with 681 residues.
gzip -f 2shkA/T0127-2shkA-2track-global.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0127-2shkA-vit.pw \
	-i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -92.618736
Database has 3 sequences with 681 residues.
gzip -f 2shkA/T0127-2shkA-vit.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/2shkA-T0127-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17812/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:        -80.445389
Database has 3 sequences with 681 residues.
gzip -f 2shkA/2shkA-T0127-vit.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/T0127-2shkA-global.pw -i T0127.t2k-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0127.t2k-w0.5.mod
T0127.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28182/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:        -87.262337
Database has 3 sequences with 681 residues.
gzip -f 2shkA/T0127-2shkA-global.pw.a2m
make 2shkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t127'
make[2]: `2shkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
/projects/compbio/bin/alpha.new/hmmscore 2shkA/2shkA-T0127-global.pw -i /projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod -db T0127.seq -db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2s/2shkA/info/2shkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2s/2shkA/nostruct-align/2shkA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17812/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:        -85.002319
Database has 3 sequences with 681 residues.
gzip -f 2shkA/2shkA-T0127-global.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2s/2shkA/struct-align/2shkA.fssp-w0.5.mod', needed by `2shkA/2shkA-T0127-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2shkA/xxxx-2shkA-T0127-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t127'
make: [joints] Error 2 (ignored)