make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
/projects/compbio/bin/scripts/w0.5 T0114.t2k.a2m.gz T0114.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp -alignfile T0114.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file T0114.t2k.a2m.gz (2 sequences, 87 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m.
Dropping 1 (of 2) sequences with > 80.0% id
1 sequences left after dropping 1 of 2 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m (1 sequences, 87 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.mod T0114.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qh7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1qh7A
fixmode 1qh7A
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -58.750973
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-local.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99.a2m.gz (124 sequences, 207 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp.a2m.
Dropping 4 (of 124) duplicate sequences with differing IDs
Dropping 73 (of 124) sequences with > 80.0% id
47 sequences left after dropping 77 of 124 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp.a2m (47 sequences, 207 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qh7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/1qh7A-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -153.439957
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/1qh7A-T0114-local.pw.a2m
make 1qh7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -54.093639
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-vit.pw.a2m
make 1qh7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/1qh7A-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -149.188293
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/1qh7A-T0114-vit.pw.a2m
make 1qh7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -34.119030
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-global.pw.a2m
make 1qh7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/1qh7A-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qh7A/nostruct-align/1qh7A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20932/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -146.611694
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/1qh7A-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp.a2m.gz (7 sequences, 247 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/tmp.a2m.
Dropping 2 (of 7) sequences with > 80.0% id
5 sequences left after dropping 2 of 7 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/tmp.a2m (5 sequences, 247 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1qtsA
fixmode 1qtsA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/1qtsA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qtsA/struct-align/1qtsA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17286/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -192.333374
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/1qtsA-T0114-fssp-global.pw.a2m
make 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.078140
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/1qtsA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14228/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -203.820450
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/1qtsA-T0114-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.045460
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-vit.pw.a2m
make 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/1qtsA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14228/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -201.544800
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/1qtsA-T0114-vit.pw.a2m
make 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -19.765676
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-global.pw.a2m
make 1qtsA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/1qtsA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qtsA/nostruct-align/1qtsA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14228/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -196.108688
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/1qtsA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp.a2m.gz (50 sequences, 393 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp.a2m.
Dropping 18 (of 50) duplicate sequences with differing IDs
Dropping 16 (of 50) sequences with > 80.0% id
16 sequences left after dropping 34 of 50 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp.a2m (16 sequences, 393 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1axkA
fixmode 1axkA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/1axkA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -268.606354
Database has 3 sequences with 874 residues.
gzip -f 1axkA/1axkA-T0114-fssp-global.pw.a2m
make 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.873753
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-local.pw.a2m
make 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/1axkA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26573/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -248.963074
Database has 3 sequences with 874 residues.
gzip -f 1axkA/1axkA-T0114-local.pw.a2m
make 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -52.101734
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-vit.pw.a2m
make 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/1axkA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26573/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -245.155746
Database has 3 sequences with 874 residues.
gzip -f 1axkA/1axkA-T0114-vit.pw.a2m
make 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        2.943268
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-global.pw.a2m
make 1axkA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/1axkA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26573/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01
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:        -243.054733
Database has 3 sequences with 874 residues.
gzip -f 1axkA/1axkA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0114.t2k.2d.rdb T0114.t2k-2d.mod
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
Error in locating FIM delete in 1qh7A
Error in locating FIM delete in 1qh7A
.
Average NLL-Simple NULL score:        -36.573799
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make[1]: *** No rule to make target `	', needed by `joint'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
Error in locating FIM delete in 1qtsA
Error in locating FIM delete in 1qtsA
.
Average NLL-Simple NULL score:        -35.535275
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make[1]: *** No rule to make target `	', needed by `joint'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
Error in locating FIM delete in 1axkA
Error in locating FIM delete in 1axkA
.
Average NLL-Simple NULL score:        -35.565975
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make[1]: *** No rule to make target `	', needed by `joint'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
Error in locating FIM delete in 1qh7A
Error in locating FIM delete in 1qh7A
.
Average NLL-Simple NULL score:        -36.573799
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
Error in locating FIM delete in 1qtsA
Error in locating FIM delete in 1qtsA
.
Average NLL-Simple NULL score:        -35.535275
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
Error in locating FIM delete in 1axkA
Error in locating FIM delete in 1axkA
.
Average NLL-Simple NULL score:        -35.565975
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -36.573799
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.535275
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.565975
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=bq joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/bq/1qfhA/struct-align/1qfhA.fssp-w0.5.mod', needed by `1qfhA/1qfhA-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/bq/1qfhA/info/1qfhA.stride-mixed.seq', needed by `1qfhA/T0114-1qfhA-local.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/bq/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod', needed by `1qfhA/1qfhA-T0114-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-1254


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp.a2m.gz (5 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/tmp.a2m.
Dropping 1 (of 5) duplicate sequences with differing IDs
4 sequences left after dropping 1 of 5 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/tmp.a2m (4 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1qfhA
fixmode 1qfhA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/1qfhA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qfhA/struct-align/1qfhA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1254/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
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:        -162.544022
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/1qfhA-T0114-fssp-global.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1qfhA' has modification time in the future
make[2]: `1qfhA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.312679
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-local.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/1qfhA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21915/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -108.560005
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/1qfhA-T0114-local.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1qfhA' has modification time in the future
make[2]: `1qfhA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.125484
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-local.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1qfhA' has modification time in the future
make[2]: `1qfhA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -48.964001
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-vit.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1qfhA' has modification time in the future
make[2]: `1qfhA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/1qfhA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21915/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -105.430016
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/1qfhA-T0114-vit.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
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:        -24.099701
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-global.pw.a2m
make 1qfhA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/1qfhA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qfhA/nostruct-align/1qfhA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21915/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
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:        -103.499687
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/1qfhA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-2271


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp.a2m.gz (5 sequences, 74 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/tmp.a2m.
Dropping 3 (of 5) duplicate sequences with differing IDs
Dropping 1 (of 5) sequences with > 80.0% id
1 sequences left after dropping 4 of 5 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/tmp.a2m (1 sequences, 74 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/tmp.mod /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1hoe
fixmode 1hoe
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/1hoe-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1h/1hoe/struct-align/1hoe.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-2271/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
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:        -77.665680
Database has 3 sequences with 235 residues.
gzip -f 1hoe/1hoe-T0114-fssp-global.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -54.467667
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-local.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/1hoe-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25128/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -58.810333
Database has 3 sequences with 235 residues.
gzip -f 1hoe/1hoe-T0114-local.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.586170
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-local.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.458996
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-vit.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/1hoe-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25128/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -56.444668
Database has 3 sequences with 235 residues.
gzip -f 1hoe/1hoe-T0114-vit.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
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:        -43.053680
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-global.pw.a2m
make 1hoe
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1hoe' has modification time in the future
make[2]: `1hoe' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/1hoe-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1h/1hoe/nostruct-align/1hoe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25128/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
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:        -55.405018
Database has 3 sequences with 235 residues.
gzip -f 1hoe/1hoe-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -36.573799
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -35.535275
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -35.565975
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -35.125484
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -35.586170
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-2842


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-2842/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.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/1ap0/struct-align/1ap0.fssp.a2m.gz (1 sequences, 73 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-2842/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-2842/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-2842/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-purr-2842/tmp.a2m (1 sequences, 73 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-2842/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-purr-2842 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1ap0
fixmode 1ap0
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/1ap0-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1ap0/struct-align/1ap0.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-2842/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -72.784004
Database has 3 sequences with 233 residues.
gzip -f 1ap0/1ap0-T0114-fssp-global.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -53.266727
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-local.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1ap0' has modification time in the future
make[2]: `1ap0' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/1ap0-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6126/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -46.286732
Database has 3 sequences with 233 residues.
gzip -f 1ap0/1ap0-T0114-local.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1ap0' has modification time in the future
make[2]: `1ap0' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -38.504902
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-local.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1ap0' has modification time in the future
make[2]: `1ap0' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -50.050732
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-vit.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1ap0' has modification time in the future
make[2]: `1ap0' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/1ap0-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6126/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.146069
Database has 3 sequences with 233 residues.
gzip -f 1ap0/1ap0-T0114-vit.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1ap0' has modification time in the future
make[2]: `1ap0' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -44.092346
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-global.pw.a2m
make 1ap0
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1ap0' has modification time in the future
make[2]: `1ap0' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/1ap0-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1ap0/nostruct-align/1ap0.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6126/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -42.488678
Database has 3 sequences with 233 residues.
gzip -f 1ap0/1ap0-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-2891


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-2891/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.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/1e/1epaA/struct-align/1epaA.fssp.a2m.gz (14 sequences, 151 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-2891/tmp.a2m.
Dropping 2 (of 14) duplicate sequences with differing IDs
Dropping 1 (of 14) sequences with > 80.0% id
11 sequences left after dropping 3 of 14 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-2891/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-2891/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-purr-2891/tmp.a2m (11 sequences, 151 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-2891/tmp.mod /projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-purr-2891 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1epaA
fixmode 1epaA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/1epaA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1epaA/struct-align/1epaA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-2891/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -75.302696
Database has 3 sequences with 411 residues.
gzip -f 1epaA/1epaA-T0114-fssp-global.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1epaA' has modification time in the future
make[2]: `1epaA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -52.869370
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-local.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/1epaA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11074/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -74.135704
Database has 3 sequences with 411 residues.
gzip -f 1epaA/1epaA-T0114-local.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1epaA' has modification time in the future
make[2]: `1epaA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -38.059536
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-local.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1epaA' has modification time in the future
make[2]: `1epaA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.942036
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-vit.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1epaA' has modification time in the future
make[2]: `1epaA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/1epaA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11074/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -70.572372
Database has 3 sequences with 411 residues.
gzip -f 1epaA/1epaA-T0114-vit.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1epaA' has modification time in the future
make[2]: `1epaA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -31.114676
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-global.pw.a2m
make 1epaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/1epaA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1epaA/nostruct-align/1epaA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11074/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -66.752014
Database has 3 sequences with 411 residues.
gzip -f 1epaA/1epaA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-2940


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-2940/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.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/1gsoA/struct-align/1gsoA.fssp.a2m.gz (9 sequences, 419 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-2940/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-2940/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-2940/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-purr-2940/tmp.a2m (9 sequences, 419 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-2940/tmp.mod /projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-purr-2940 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
mkdir 1gsoA
fixmode 1gsoA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/1gsoA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gsoA/struct-align/1gsoA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-2940/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -250.924728
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/1gsoA-T0114-fssp-global.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -53.077732
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-local.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1gsoA' has modification time in the future
make[2]: `1gsoA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/1gsoA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23549/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -213.022095
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/1gsoA-T0114-local.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -37.969418
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-local.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1gsoA' has modification time in the future
make[2]: `1gsoA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -48.899750
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-vit.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: *** Warning: File `1gsoA' has modification time in the future
make[2]: `1gsoA' is up to date.
make[2]: *** Warning:  Clock skew detected.  Your build may be incomplete.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/1gsoA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23549/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -209.618423
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/1gsoA-T0114-vit.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        8.885284
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-global.pw.a2m
make 1gsoA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/1gsoA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gsoA/nostruct-align/1gsoA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23549/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
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:        -199.508377
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/1gsoA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3149.234375
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        4200.515625
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        8090.091309
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3292.268799
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -27.182013
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -30.333014
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        1904.323242
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        8747.065430
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1wapA PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(545):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -23.304174
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wapA/xxxx-1wapA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -36.569302
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3149.315186
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.481113
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        4200.560547
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.614315
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        8090.130371
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.139297
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-local.pw.a2m
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3292.298096
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.613998
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-local.pw.a2m
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -27.157015
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -38.429062
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-local.pw.a2m
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -30.286339
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.914371
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-local.pw.a2m
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        1904.307983
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.881748
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-local.pw.a2m
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        8747.086914
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1wapA PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -35.152592
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-local.pw.a2m
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -23.305510
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wapA/xxxx-1wapA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1wapA PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wapA/xxxx-1wapA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.219128
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3122.571045
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -44.170959
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        4190.671387
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.775982
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        8041.697754
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.399799
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-local.pw.a2m
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3265.474609
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.680157
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-local.pw.a2m
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -41.018177
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -44.458893
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-local.pw.a2m
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.635841
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.696369
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-local.pw.a2m
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        1894.205444
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -43.311420
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-local.pw.a2m
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        8764.260742
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1wapA PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.228588
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-local.pw.a2m
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.432171
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wapA/xxxx-1wapA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1wapA PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wapA/xxxx-1wapA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1aozA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22475


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22475/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.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/1aozA/struct-align/1aozA.fssp.a2m.gz (16 sequences, 552 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22475/tmp.a2m.
Dropping 7 (of 16) duplicate sequences with differing IDs
9 sequences left after dropping 7 of 16 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22475/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22475/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-22475/tmp.a2m (9 sequences, 552 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22475/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22475 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1aozA
fixmode 1aozA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/1aozA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aozA/struct-align/1aozA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22475/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -428.933105
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/1aozA-T0114-fssp-global.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.742035
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-local.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/1aozA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12490/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -345.149292
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/1aozA-T0114-local.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.641155
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-2track-local.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        12259.617188
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-2track-global.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.950054
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-vit.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/1aozA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12490/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -341.266022
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/1aozA-T0114-vit.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        26.230255
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-global.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/1aozA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aozA/nostruct-align/1aozA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12490/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -331.912720
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/1aozA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aozA/xxxx-1aozA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1avmA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13404


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13404/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.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/1avmA/struct-align/1avmA.fssp.a2m.gz (63 sequences, 201 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13404/tmp.a2m.
Dropping 46 (of 63) duplicate sequences with differing IDs
Dropping 6 (of 63) sequences with > 80.0% id
11 sequences left after dropping 52 of 63 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13404/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13404/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-13404/tmp.a2m (11 sequences, 201 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13404/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13404 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1avmA
fixmode 1avmA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/1avmA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1avmA/struct-align/1avmA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13404/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -140.391342
Database has 3 sequences with 489 residues.
gzip -f 1avmA/1avmA-T0114-fssp-global.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.178844
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-local.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/1avmA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25598/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -132.116531
Database has 3 sequences with 489 residues.
gzip -f 1avmA/1avmA-T0114-local.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.373657
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-2track-local.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        2994.716064
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-2track-global.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.665508
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-vit.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/1avmA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25598/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -128.690201
Database has 3 sequences with 489 residues.
gzip -f 1avmA/1avmA-T0114-vit.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -26.045013
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-global.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/1avmA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1avmA/nostruct-align/1avmA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25598/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -125.957336
Database has 3 sequences with 489 residues.
gzip -f 1avmA/1avmA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1avmA/xxxx-1avmA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1d4vA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25746


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25746/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.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/1d/1d4vA/struct-align/1d4vA.fssp.a2m.gz (5 sequences, 117 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25746/tmp.a2m.
Dropping 1 (of 5) duplicate sequences with differing IDs
Dropping 2 (of 5) sequences with > 80.0% id
2 sequences left after dropping 3 of 5 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25746/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25746/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-25746/tmp.a2m (2 sequences, 117 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25746/tmp.mod /projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25746 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1d4vA
fixmode 1d4vA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/1d4vA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d4vA/struct-align/1d4vA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25746/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -107.384674
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/1d4vA-T0114-fssp-global.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.868946
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-local.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/1d4vA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20440/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -68.283913
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/1d4vA-T0114-local.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -44.530750
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-2track-local.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        760.027832
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-2track-global.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.210266
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-vit.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/1d4vA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20440/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -65.028252
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/1d4vA-T0114-vit.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -38.017017
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-global.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/1d4vA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1d4vA/nostruct-align/1d4vA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20440/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -64.539337
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/1d4vA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d4vA/xxxx-1d4vA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qksA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1qksA
fixmode 1qksA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/1qksA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qksA/struct-align/1qksA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qksA/struct-align/1qksA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qksA/struct-align/1qksA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1409/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -329.507385
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/1qksA-T0114-fssp-global.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -54.619640
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-local.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/1qksA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12577/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -366.047882
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/1qksA-T0114-local.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.779095
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-2track-local.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        12462.887695
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-2track-global.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.623638
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-vit.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/1qksA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12577/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -362.490875
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/1qksA-T0114-vit.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        30.855906
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-global.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/1qksA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qksA/nostruct-align/1qksA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12577/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -359.954437
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/1qksA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qksA/xxxx-1qksA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1uok  PRED2=1u joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25779


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25779/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.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/1u/1uok/struct-align/1uok.fssp.a2m.gz (61 sequences, 558 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25779/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25779/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25779/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-25779/tmp.a2m (61 sequences, 558 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25779/tmp.mod /projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25779 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1uok
fixmode 1uok
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/1uok-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1u/1uok/struct-align/1uok.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25779/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -225.088058
Database has 3 sequences with 1203 residues.
gzip -f 1uok/1uok-T0114-fssp-global.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.303558
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-local.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/1uok-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6837/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -321.635834
Database has 3 sequences with 1203 residues.
gzip -f 1uok/1uok-T0114-local.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.283649
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-2track-local.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        12442.567383
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-2track-global.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.061543
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-vit.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/1uok-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6837/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -318.067200
Database has 3 sequences with 1203 residues.
gzip -f 1uok/1uok-T0114-vit.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        28.418243
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-global.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/1uok-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1u/1uok/nostruct-align/1uok.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6837/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -303.495728
Database has 3 sequences with 1203 residues.
gzip -f 1uok/1uok-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1uok/xxxx-1uok-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1fuiA PRED2=1f joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24513


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24513/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.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/1f/1fuiA/struct-align/1fuiA.fssp.a2m.gz (46 sequences, 591 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24513/tmp.a2m.
Dropping 5 (of 46) duplicate sequences with differing IDs
41 sequences left after dropping 5 of 46 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24513/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24513/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-24513/tmp.a2m (41 sequences, 591 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24513/tmp.mod /projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24513 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1fuiA
fixmode 1fuiA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/1fuiA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1f/1fuiA/struct-align/1fuiA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24513/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -315.501373
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/1fuiA-T0114-fssp-global.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -54.295177
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-local.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/1fuiA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20361/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -522.894226
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/1fuiA-T0114-local.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -46.240032
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-2track-local.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        13313.651367
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-2track-global.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -50.101177
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-vit.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/1fuiA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20361/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -520.110535
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/1fuiA-T0114-vit.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        35.988964
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-global.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/1fuiA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1f/1fuiA/nostruct-align/1fuiA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20361/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -500.290070
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/1fuiA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fuiA/xxxx-1fuiA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1jmcA PRED2=1j joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25845


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25845/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.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/1j/1jmcA/struct-align/1jmcA.fssp.a2m.gz (9 sequences, 238 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25845/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25845/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25845/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-25845/tmp.a2m (9 sequences, 238 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25845/tmp.mod /projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25845 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1jmcA
fixmode 1jmcA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/1jmcA-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1j/1jmcA/struct-align/1jmcA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25845/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -152.319351
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/1jmcA-T0114-fssp-global.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.098522
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-local.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/1jmcA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20969/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -145.718185
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/1jmcA-T0114-local.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -46.853668
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-2track-local.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3959.711670
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-2track-global.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -48.375854
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-vit.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/1jmcA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20969/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -142.478195
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/1jmcA-T0114-vit.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -18.082022
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-global.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/1jmcA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1j/1jmcA/nostruct-align/1jmcA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20969/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -137.771698
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/1jmcA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1jmcA/xxxx-1jmcA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1clc  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25847


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25847/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.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/1clc/struct-align/1clc.fssp.a2m.gz (12 sequences, 541 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25847/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25847/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25847/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-25847/tmp.a2m (12 sequences, 541 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25847/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25847 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1clc
fixmode 1clc
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/1clc-T0114-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.fssp-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1clc/struct-align/1clc.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25847/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -332.527069
Database has 3 sequences with 1267 residues.
gzip -f 1clc/1clc-T0114-fssp-global.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.162609
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-local.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/1clc-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3775/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -288.538574
Database has 3 sequences with 1267 residues.
gzip -f 1clc/1clc-T0114-local.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -46.444092
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-2track-local.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.2d \
	-fim_method_score 5 -inset_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Command line option(18):  Could not understand inset_method_score 5
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        11996.331055
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-2track-global.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -48.445251
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-vit.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/1clc-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3775/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -284.411926
Database has 3 sequences with 1267 residues.
gzip -f 1clc/1clc-T0114-vit.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        34.902943
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-global.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/1clc-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1clc/nostruct-align/1clc.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3775/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -270.882050
Database has 3 sequences with 1267 residues.
gzip -f 1clc/1clc-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1clc/xxxx-1clc-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qh7A PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qh7A/struct-align/1qh7A.fssp-w0.5.mod', needed by `1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz'.
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.967468
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-local.pw.a2m
make 1qh7A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qh7A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qh7A/T0114-1qh7A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qh7A/info/1qh7A.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -28.637192
Database has 3 sequences with 502 residues.
gzip -f 1qh7A/T0114-1qh7A-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qh7A/xxxx-1qh7A-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qtsA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -44.813965
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-local.pw.a2m
make 1qtsA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qtsA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qtsA/T0114-1qtsA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qtsA/info/1qtsA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15.772883
Database has 3 sequences with 581 residues.
gzip -f 1qtsA/T0114-1qtsA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qtsA/xxxx-1qtsA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1axkA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.026325
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-local.pw.a2m
make 1axkA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1axkA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1axkA/T0114-1axkA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        7.117640
Database has 3 sequences with 874 residues.
gzip -f 1axkA/T0114-1axkA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qfhA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -46.456135
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-local.pw.a2m
make 1qfhA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qfhA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qfhA/T0114-1qfhA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qfhA/info/1qfhA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -19.978510
Database has 3 sequences with 511 residues.
gzip -f 1qfhA/T0114-1qfhA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qfhA/xxxx-1qfhA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1hoe PRED2=1h joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.943829
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-local.pw.a2m
make 1hoe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1hoe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1hoe/T0114-1hoe-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hoe/info/1hoe.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.079178
Database has 3 sequences with 235 residues.
gzip -f 1hoe/T0114-1hoe-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hoe/xxxx-1hoe-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1ap0 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -44.774567
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-local.pw.a2m
make 1ap0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1ap0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1ap0/T0114-1ap0-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1ap0/info/1ap0.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -38.914181
Database has 3 sequences with 233 residues.
gzip -f 1ap0/T0114-1ap0-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ap0/xxxx-1ap0-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1epaA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.888042
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-local.pw.a2m
make 1epaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1epaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1epaA/T0114-1epaA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1epaA/info/1epaA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -28.008682
Database has 3 sequences with 411 residues.
gzip -f 1epaA/T0114-1epaA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1epaA/xxxx-1epaA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1gsoA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -43.829426
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-local.pw.a2m
make 1gsoA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1gsoA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1gsoA/T0114-1gsoA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gsoA/info/1gsoA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        27.125635
Database has 3 sequences with 937 residues.
gzip -f 1gsoA/T0114-1gsoA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gsoA/xxxx-1gsoA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1wapA PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.453922
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-local.pw.a2m
make 1wapA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1wapA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1wapA/T0114-1wapA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wapA/info/1wapA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -38.884506
Database has 3 sequences with 232 residues.
gzip -f 1wapA/T0114-1wapA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wapA/xxxx-1wapA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1aozA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -48.131531
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-2track-local.pw.a2m
make 1aozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1aozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1aozA/T0114-1aozA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aozA/info/1aozA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        31.212103
Database has 3 sequences with 1191 residues.
gzip -f 1aozA/T0114-1aozA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aozA/xxxx-1aozA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1avmA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.518658
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-2track-local.pw.a2m
make 1avmA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1avmA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1avmA/T0114-1avmA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1avmA/info/1avmA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12.514847
Database has 3 sequences with 489 residues.
gzip -f 1avmA/T0114-1avmA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1avmA/xxxx-1avmA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1d4vA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -45.063091
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-2track-local.pw.a2m
make 1d4vA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1d4vA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1d4vA/T0114-1d4vA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d4vA/info/1d4vA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -32.251846
Database has 3 sequences with 321 residues.
gzip -f 1d4vA/T0114-1d4vA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d4vA/xxxx-1d4vA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1qksA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -50.234760
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-2track-local.pw.a2m
make 1qksA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1qksA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1qksA/T0114-1qksA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qksA/info/1qksA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        49.950100
Database has 3 sequences with 1213 residues.
gzip -f 1qksA/T0114-1qksA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qksA/xxxx-1qksA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1uok  PRED2=1u joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.522644
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-2track-local.pw.a2m
make 1uok
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1uok' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1uok/T0114-1uok-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1uok/info/1uok.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        42.719833
Database has 3 sequences with 1203 residues.
gzip -f 1uok/T0114-1uok-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1uok/xxxx-1uok-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1fuiA PRED2=1f joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -46.561707
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-2track-local.pw.a2m
make 1fuiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1fuiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1fuiA/T0114-1fuiA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fuiA/info/1fuiA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        45.788437
Database has 3 sequences with 1269 residues.
gzip -f 1fuiA/T0114-1fuiA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fuiA/xxxx-1fuiA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1jmcA PRED2=1j joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -48.652008
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-2track-local.pw.a2m
make 1jmcA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1jmcA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1jmcA/T0114-1jmcA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1j/1jmcA/info/1jmcA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12.722844
Database has 3 sequences with 571 residues.
gzip -f 1jmcA/T0114-1jmcA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1jmcA/xxxx-1jmcA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1clc  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -46.833111
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-2track-local.pw.a2m
make 1clc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1clc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1clc/T0114-1clc-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1clc/info/1clc.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        37.914780
Database has 3 sequences with 1267 residues.
gzip -f 1clc/T0114-1clc-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1clc/xxxx-1clc-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1xnb  PRED2=1x joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1x/1xnb/struct-align/1xnb.fssp-w0.5.mod', needed by `1xnb/1xnb-T0114-fssp-global.pw.a2m.gz'.
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1xnb
fixmode 1xnb
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/T0114-1xnb-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -56.404144
Database has 3 sequences with 457 residues.
gzip -f 1xnb/T0114-1xnb-local.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/1xnb-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19572/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -131.823166
Database has 3 sequences with 457 residues.
gzip -f 1xnb/1xnb-T0114-local.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/T0114-1xnb-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq,/projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.182293
Database has 3 sequences with 457 residues.
gzip -f 1xnb/T0114-1xnb-2track-local.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/T0114-1xnb-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq,/projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -32.170506
Database has 3 sequences with 457 residues.
gzip -f 1xnb/T0114-1xnb-2track-global.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/T0114-1xnb-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -52.636169
Database has 3 sequences with 457 residues.
gzip -f 1xnb/T0114-1xnb-vit.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/1xnb-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19572/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -128.230835
Database has 3 sequences with 457 residues.
gzip -f 1xnb/1xnb-T0114-vit.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/T0114-1xnb-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -33.051037
Database has 3 sequences with 457 residues.
gzip -f 1xnb/T0114-1xnb-global.pw.a2m
make 1xnb
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1xnb' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1xnb/1xnb-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1x/1xnb/info/1xnb.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1x/1xnb/nostruct-align/1xnb.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19572/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -126.585693
Database has 3 sequences with 457 residues.
gzip -f 1xnb/1xnb-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1xnb/xxxx-1xnb-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1obwA PRED2=1o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1o/1obwA/struct-align/1obwA.fssp-w0.5.mod', needed by `1obwA/1obwA-T0114-fssp-global.pw.a2m.gz'.
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1obwA
fixmode 1obwA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/T0114-1obwA-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.106518
Database has 3 sequences with 437 residues.
gzip -f 1obwA/T0114-1obwA-local.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/1obwA-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17664/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -113.620201
Database has 3 sequences with 437 residues.
gzip -f 1obwA/1obwA-T0114-local.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/T0114-1obwA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -47.432354
Database has 3 sequences with 437 residues.
gzip -f 1obwA/T0114-1obwA-2track-local.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/T0114-1obwA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -29.422195
Database has 3 sequences with 437 residues.
gzip -f 1obwA/T0114-1obwA-2track-global.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/T0114-1obwA-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.682514
Database has 3 sequences with 437 residues.
gzip -f 1obwA/T0114-1obwA-vit.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/1obwA-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17664/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.043541
Database has 3 sequences with 437 residues.
gzip -f 1obwA/1obwA-T0114-vit.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/T0114-1obwA-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -30.804352
Database has 3 sequences with 437 residues.
gzip -f 1obwA/T0114-1obwA-global.pw.a2m
make 1obwA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1obwA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1obwA/1obwA-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1o/1obwA/info/1obwA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1o/1obwA/nostruct-align/1obwA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17664/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -107.998360
Database has 3 sequences with 437 residues.
gzip -f 1obwA/1obwA-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1obwA/xxxx-1obwA-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)
make -k PRED=1lnh  PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1l/1lnh/struct-align/1lnh.fssp-w0.5.mod', needed by `1lnh/1lnh-T0114-fssp-global.pw.a2m.gz'.
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
mkdir 1lnh
fixmode 1lnh
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/T0114-1lnh-local.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -53.408783
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/T0114-1lnh-local.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/1lnh-T0114-local.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25882/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -611.804504
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/1lnh-T0114-local.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/T0114-1lnh-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.177715
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/T0114-1lnh-2track-local.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/T0114-1lnh-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0114.t2k-w0.5.mod,T0114.t2k-2d.mod \
 -db T0114.seq,T0114.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0114.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0114.t2k-2d.mod(551):  Reading track 1 model from MODEL -- Model from 2nd structure file T0114.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        75.176659
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/T0114-1lnh-2track-global.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/T0114-1lnh-vit.pw \
	-i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -49.643818
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/T0114-1lnh-vit.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/1lnh-T0114-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25882/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -608.495789
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/1lnh-T0114-vit.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/T0114-1lnh-global.pw -i T0114.t2k-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0114.t2k-w0.5.mod
T0114.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-8279/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        74.106880
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/T0114-1lnh-global.pw.a2m
make 1lnh
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t114'
make[2]: `1lnh' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
hmmscore 1lnh/1lnh-T0114-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod -db T0114.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lnh/info/1lnh.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lnh/nostruct-align/1lnh.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25882/tmp.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
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:        -578.935059
Database has 3 sequences with 1780 residues.
gzip -f 1lnh/1lnh-T0114-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lnh/xxxx-1lnh-T0114-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t114'
make: [joints] Error 2 (ignored)