make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
gzip -f T0103.t2k_trimmed.a2m
/projects/compbio/bin/scripts/w0.5 T0103.t2k_trimmed.a2m.gz T0103.t2k_trimmed-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4832


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp -alignfile T0103.t2k_trimmed.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file T0103.t2k_trimmed.a2m.gz (72 sequences, 372 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m.
Dropping 6 (of 72) duplicate sequences with differing IDs
Dropping 17 (of 72) sequences with > 80.0% id
49 sequences left after dropping 23 of 72 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m (49 sequences, 372 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.mod T0103.t2k_trimmed-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4832 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
mkdir 1thm
fixmode 1thm
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-local.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -217.935928
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t2k-w0.5.mod', needed by `1thm/1thm-T0103-local.pw.a2m.gz'.
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-vit.pw \
	-i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -214.939926
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-vit.pw.a2m
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-global.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -328.949371
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
mkdir 1s01
fixmode 1s01
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-local.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -232.484879
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t2k-w0.5.mod', needed by `1s01/1s01-T0103-local.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-vit.pw \
	-i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -228.909561
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-vit.pw.a2m
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-global.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -342.734009
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
mkdir 1sup
fixmode 1sup
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-local.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -233.052872
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t2k-w0.5.mod', needed by `1sup/1sup-T0103-local.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-vit.pw \
	-i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -229.337540
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-vit.pw.a2m
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-global.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -343.319336
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
mkdir 1a1yE
fixmode 1a1yE
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-local.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -227.323349
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t2k-w0.5.mod', needed by `1a1yE/1a1yE-T0103-local.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-vit.pw \
	-i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -223.867371
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-vit.pw.a2m
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-global.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -337.650726
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6158


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp.a2m.gz (83 sequences, 269 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/tmp.a2m.
Dropping 39 (of 83) duplicate sequences with differing IDs
Dropping 31 (of 83) sequences with > 80.0% id
13 sequences left after dropping 70 of 83 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/tmp.a2m (13 sequences, 269 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/tmp.mod /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6158 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
mkdir 1gci
fixmode 1gci
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/1gci-T0103-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gci/struct-align/1gci.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6158/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -284.686005
Database has 3 sequences with 910 residues.
gzip -f 1gci/1gci-T0103-fssp-global.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-local.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -225.162247
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t2k-w0.5.mod', needed by `1gci/1gci-T0103-local.pw.a2m.gz'.
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-vit.pw \
	-i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -221.894272
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-vit.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-global.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -334.121368
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
mkdir 1dbiA
fixmode 1dbiA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-local.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -215.730453
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t2k-w0.5.mod', needed by `1dbiA/1dbiA-T0103-local.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-vit.pw \
	-i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -211.938126
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-vit.pw.a2m
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-global.pw -i T0103.t2k_trimmed-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k_trimmed-w0.5.mod
T0103.t2k_trimmed-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4832/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -325.763336
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/1thm-T0103-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13228/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -173.959915
Database has 3 sequences with 930 residues.
gzip -f 1thm/1thm-T0103-local.pw.a2m
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/1thm-T0103-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13228/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -165.435242
Database has 3 sequences with 930 residues.
gzip -f 1thm/1thm-T0103-vit.pw.a2m
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/1thm-T0103-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1thm/nostruct-align/1thm.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13228/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -168.709045
Database has 3 sequences with 930 residues.
gzip -f 1thm/1thm-T0103-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/1s01-T0103-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7402/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -186.277527
Database has 3 sequences with 922 residues.
gzip -f 1s01/1s01-T0103-local.pw.a2m
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/1s01-T0103-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7402/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -181.601883
Database has 3 sequences with 922 residues.
gzip -f 1s01/1s01-T0103-vit.pw.a2m
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/1s01-T0103-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1s01/nostruct-align/1s01.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7402/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -180.078690
Database has 3 sequences with 922 residues.
gzip -f 1s01/1s01-T0103-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/1sup-T0103-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-15142/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -182.352890
Database has 3 sequences with 922 residues.
gzip -f 1sup/1sup-T0103-local.pw.a2m
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/1sup-T0103-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-15142/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -177.020569
Database has 3 sequences with 922 residues.
gzip -f 1sup/1sup-T0103-vit.pw.a2m
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/1sup-T0103-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1s/1sup/nostruct-align/1sup.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-15142/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -176.381042
Database has 3 sequences with 922 residues.
gzip -f 1sup/1sup-T0103-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/1a1yE-T0103-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17300/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -175.474319
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/1a1yE-T0103-local.pw.a2m
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/1a1yE-T0103-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17300/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -169.152664
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/1a1yE-T0103-vit.pw.a2m
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/1a1yE-T0103-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a1yE/nostruct-align/1a1yE.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-17300/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -168.925369
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/1a1yE-T0103-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/1gci-T0103-local.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3956/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -174.190903
Database has 3 sequences with 910 residues.
gzip -f 1gci/1gci-T0103-local.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/1gci-T0103-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3956/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -167.946213
Database has 3 sequences with 910 residues.
gzip -f 1gci/1gci-T0103-vit.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/1gci-T0103-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1g/1gci/nostruct-align/1gci.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3956/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -167.381393
Database has 3 sequences with 910 residues.
gzip -f 1gci/1gci-T0103-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/1dbiA-T0103-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30031/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -169.952759
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/1dbiA-T0103-local.pw.a2m
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/1dbiA-T0103-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30031/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -163.555115
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/1dbiA-T0103-vit.pw.a2m
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/1dbiA-T0103-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbiA/nostruct-align/1dbiA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30031/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -162.422012
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/1dbiA-T0103-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
/projects/compbio/bin/scripts/w0.5 T0103.t2k.a2m.gz T0103.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25937


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp -alignfile T0103.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file T0103.t2k.a2m.gz (113 sequences, 372 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m.
Dropping 11 (of 113) duplicate sequences with differing IDs
Dropping 50 (of 113) sequences with > 80.0% id
52 sequences left after dropping 61 of 113 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m (52 sequences, 372 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.mod T0103.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25937 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-local.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -218.509232
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-local.pw.a2m
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-vit.pw \
	-i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -215.508560
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-vit.pw.a2m
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-global.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -329.256378
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-local.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -239.440231
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-local.pw.a2m
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-vit.pw \
	-i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -236.456238
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-vit.pw.a2m
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-global.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -349.425690
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-local.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -240.162231
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-local.pw.a2m
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-vit.pw \
	-i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -237.125549
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-vit.pw.a2m
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-global.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -350.158356
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-local.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -232.588669
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-local.pw.a2m
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-vit.pw \
	-i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -229.169983
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-vit.pw.a2m
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-global.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -342.752350
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-local.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -227.768921
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-local.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-vit.pw \
	-i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -224.715591
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-vit.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-global.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -336.531708
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-local.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -216.117783
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-local.pw.a2m
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-vit.pw \
	-i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -212.345444
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-vit.pw.a2m
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-global.pw -i T0103.t2k-w0.5.mod -db T0103.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0103.t2k-w0.5.mod
T0103.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -325.890015
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0103.t2k.2d.rdb T0103.t2k-2d.mod
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -168.098419
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -184.562378
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -183.742722
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -177.346512
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -175.173096
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -169.158615
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -168.098419
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -184.562378
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -183.742722
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -177.346512
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -175.173096
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -169.158615
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -168.098419
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -184.562378
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -183.742722
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -177.346512
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -175.173096
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -169.158615
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -136.212723
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -153.349045
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -151.635025
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -153.139679
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -146.457687
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/tmp.a2m
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -126.000183
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1thm PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1thm/struct-align/1thm.fssp-w0.5.mod', needed by `1thm/1thm-T0103-fssp-global.pw.a2m.gz'.
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.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
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12383.257813
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-2track-local.pw.a2m
make 1thm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1thm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1thm/T0103-1thm-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1thm/info/1thm.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12386.725586
Database has 3 sequences with 930 residues.
gzip -f 1thm/T0103-1thm-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1thm/xxxx-1thm-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1s01 PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1s01/struct-align/1s01.fssp-w0.5.mod', needed by `1s01/1s01-T0103-fssp-global.pw.a2m.gz'.
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.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
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12296.859375
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-2track-local.pw.a2m
make 1s01
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1s01' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1s01/T0103-1s01-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1s01/info/1s01.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12297.782227
Database has 3 sequences with 922 residues.
gzip -f 1s01/T0103-1s01-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1s01/xxxx-1s01-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1sup PRED2=1s joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sup/struct-align/1sup.fssp-w0.5.mod', needed by `1sup/1sup-T0103-fssp-global.pw.a2m.gz'.
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.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
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12294.219727
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-2track-local.pw.a2m
make 1sup
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1sup' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1sup/T0103-1sup-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sup/info/1sup.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12295.135742
Database has 3 sequences with 922 residues.
gzip -f 1sup/T0103-1sup-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sup/xxxx-1sup-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1a1yE PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a1yE/struct-align/1a1yE.fssp-w0.5.mod', needed by `1a1yE/1a1yE-T0103-fssp-global.pw.a2m.gz'.
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.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
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12269.817383
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-2track-local.pw.a2m
make 1a1yE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1a1yE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1a1yE/T0103-1a1yE-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a1yE/info/1a1yE.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12270.992188
Database has 3 sequences with 920 residues.
gzip -f 1a1yE/T0103-1a1yE-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a1yE/xxxx-1a1yE-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1gci PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.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
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12133.676758
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-2track-local.pw.a2m
make 1gci
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1gci' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1gci/T0103-1gci-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gci/info/1gci.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12135.101563
Database has 3 sequences with 910 residues.
gzip -f 1gci/T0103-1gci-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gci/xxxx-1gci-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)
make -k PRED=1dbiA PRED2=1d joint	
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbiA/struct-align/1dbiA.fssp-w0.5.mod', needed by `1dbiA/1dbiA-T0103-fssp-global.pw.a2m.gz'.
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.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
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12158.519531
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-2track-local.pw.a2m
make 1dbiA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t103'
make[2]: `1dbiA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
hmmscore 1dbiA/T0103-1dbiA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0103.t2k-w0.5.mod,T0103.t2k-2d.mod \
 -db T0103.seq,T0103.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbiA/info/1dbiA.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.
T0103.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25937/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.
T0103.t2k-2d.mod(2255):  Reading track 1 model from MODEL -- Model from 2nd structure file T0103.t2k.2d.rdb
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.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -12161.917969
Database has 3 sequences with 923 residues.
gzip -f 1dbiA/T0103-1dbiA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbiA/xxxx-1dbiA-T0103-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t103'
make: [joints] Error 2 (ignored)