make -k PRED=1pht PRED2=1p joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1p/1pht/struct-align/1pht.fssp-w0.5.mod', needed by `1pht/1pht-T0099-fssp-global.pw.a2m.gz'.
/projects/compbio/bin/scripts/w0.5 T0099.t2k.a2m.gz T0099.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/tmp -alignfile T0099.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 T0099.t2k.a2m.gz (871 sequences, 56 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/tmp.a2m.
Dropping 377 (of 871) duplicate sequences with differing IDs
Dropping 215 (of 871) sequences with > 80.0% id
279 sequences left after dropping 592 of 871 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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-titanic-5826/tmp.a2m (279 sequences, 56 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/tmp.mod T0099.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1pht
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
mkdir 1pht
fixmode 1pht
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1pht/T0099-1pht-local.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -36.270729
Database has 3 sequences with 224 residues.
gzip -f 1pht/T0099-1pht-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t2k-w0.5.mod', needed by `1pht/1pht-T0099-local.pw.a2m.gz'.
make 1pht
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1pht' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1pht/T0099-1pht-vit.pw \
	-i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -31.594061
Database has 3 sequences with 224 residues.
gzip -f 1pht/T0099-1pht-vit.pw.a2m
make 1pht
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1pht' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1pht/T0099-1pht-global.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -58.444004
Database has 3 sequences with 224 residues.
gzip -f 1pht/T0099-1pht-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pht/xxxx-1pht-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1ckaA PRED2=1c joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.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/1c/1ckaA/struct-align/1ckaA.fssp.a2m.gz (61 sequences, 56 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148/tmp.a2m.
Dropping 31 (of 61) duplicate sequences with differing IDs
Dropping 13 (of 61) sequences with > 80.0% id
17 sequences left after dropping 44 of 61 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148/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-titanic-6148/tmp.a2m (17 sequences, 56 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1ckaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
mkdir 1ckaA
fixmode 1ckaA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/1ckaA-T0099-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.fssp-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1ckaA/struct-align/1ckaA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-6148/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:        -45.055344
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/1ckaA-T0099-fssp-global.pw.a2m
make 1ckaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1ckaA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/T0099-1ckaA-local.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -44.850189
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/T0099-1ckaA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t2k-w0.5.mod', needed by `1ckaA/1ckaA-T0099-local.pw.a2m.gz'.
make 1ckaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1ckaA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/T0099-1ckaA-vit.pw \
	-i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -42.441193
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/T0099-1ckaA-vit.pw.a2m
make 1ckaA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1ckaA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/T0099-1ckaA-global.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -63.600018
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/T0099-1ckaA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckaA/xxxx-1ckaA-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1bbzA PRED2=1b joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.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/1b/1bbzA/struct-align/1bbzA.fssp.a2m.gz (37 sequences, 58 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234/tmp.a2m.
Dropping 14 (of 37) duplicate sequences with differing IDs
Dropping 11 (of 37) sequences with > 80.0% id
12 sequences left after dropping 25 of 37 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234/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-titanic-6234/tmp.a2m (12 sequences, 58 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1bbzA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
mkdir 1bbzA
fixmode 1bbzA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/1bbzA-T0099-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.fssp-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bbzA/struct-align/1bbzA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-6234/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:        -48.102676
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/1bbzA-T0099-fssp-global.pw.a2m
make 1bbzA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1bbzA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/T0099-1bbzA-local.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -42.749939
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/T0099-1bbzA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t2k-w0.5.mod', needed by `1bbzA/1bbzA-T0099-local.pw.a2m.gz'.
make 1bbzA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1bbzA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/T0099-1bbzA-vit.pw \
	-i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -39.918941
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/T0099-1bbzA-vit.pw.a2m
make 1bbzA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1bbzA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/T0099-1bbzA-global.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -59.757343
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/T0099-1bbzA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bbzA/xxxx-1bbzA-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1bb9 PRED2=1b joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.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/1b/1bb9/struct-align/1bb9.fssp.a2m.gz (12 sequences, 83 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296/tmp.a2m.
Dropping 3 (of 12) duplicate sequences with differing IDs
Dropping 1 (of 12) sequences with > 80.0% id
8 sequences left after dropping 4 of 12 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296/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-titanic-6296/tmp.a2m (8 sequences, 83 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1bb9
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
mkdir 1bb9
fixmode 1bb9
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/1bb9-T0099-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.fssp-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bb9/struct-align/1bb9.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-6296/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:        -67.422005
Database has 3 sequences with 254 residues.
gzip -f 1bb9/1bb9-T0099-fssp-global.pw.a2m
make 1bb9
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1bb9' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/T0099-1bb9-local.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -35.936298
Database has 3 sequences with 254 residues.
gzip -f 1bb9/T0099-1bb9-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t2k-w0.5.mod', needed by `1bb9/1bb9-T0099-local.pw.a2m.gz'.
make 1bb9
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1bb9' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/T0099-1bb9-vit.pw \
	-i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -31.383963
Database has 3 sequences with 254 residues.
gzip -f 1bb9/T0099-1bb9-vit.pw.a2m
make 1bb9
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1bb9' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/T0099-1bb9-global.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -59.905350
Database has 3 sequences with 254 residues.
gzip -f 1bb9/T0099-1bb9-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bb9/xxxx-1bb9-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1awj PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.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/1a/1awj/struct-align/1awj.fssp.a2m.gz (1 sequences, 77 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135/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-titanic-6135/tmp.a2m (1 sequences, 77 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1awj
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
mkdir 1awj
fixmode 1awj
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/1awj-T0099-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.fssp-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1awj/struct-align/1awj.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-6135/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:        -120.321693
Database has 3 sequences with 210 residues.
gzip -f 1awj/1awj-T0099-fssp-global.pw.a2m
make 1awj
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1awj' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/T0099-1awj-local.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -38.560352
Database has 3 sequences with 210 residues.
gzip -f 1awj/T0099-1awj-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t2k-w0.5.mod', needed by `1awj/1awj-T0099-local.pw.a2m.gz'.
make 1awj
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1awj' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/T0099-1awj-vit.pw \
	-i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -36.106686
Database has 3 sequences with 210 residues.
gzip -f 1awj/T0099-1awj-vit.pw.a2m
make 1awj
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1awj' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/T0099-1awj-global.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -57.251354
Database has 3 sequences with 210 residues.
gzip -f 1awj/T0099-1awj-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1awj/xxxx-1awj-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1aojA PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.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/1a/1aojA/struct-align/1aojA.fssp.a2m.gz (2 sequences, 60 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089/tmp.a2m.
Dropping 1 (of 2) duplicate sequences with differing IDs
1 sequences left after dropping 1 of 2 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089/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-titanic-6089/tmp.a2m (1 sequences, 60 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1aojA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
mkdir 1aojA
fixmode 1aojA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/1aojA-T0099-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.fssp-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aojA/struct-align/1aojA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-6089/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:        -95.932007
Database has 3 sequences with 176 residues.
gzip -f 1aojA/1aojA-T0099-fssp-global.pw.a2m
make 1aojA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1aojA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/T0099-1aojA-local.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -40.839333
Database has 3 sequences with 176 residues.
gzip -f 1aojA/T0099-1aojA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t2k-w0.5.mod', needed by `1aojA/1aojA-T0099-local.pw.a2m.gz'.
make 1aojA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1aojA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/T0099-1aojA-vit.pw \
	-i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -37.781002
Database has 3 sequences with 176 residues.
gzip -f 1aojA/T0099-1aojA-vit.pw.a2m
make 1aojA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t99'
make[2]: `1aojA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/T0099-1aojA-global.pw -i T0099.t2k-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0099.t2k-w0.5.mod
T0099.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-titanic-5826/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:        -57.974682
Database has 3 sequences with 176 residues.
gzip -f 1aojA/T0099-1aojA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aojA/xxxx-1aojA-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1pht PRED2=1p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1p/1pht/struct-align/1pht.fssp-w0.5.mod', needed by `1pht/1pht-T0099-fssp-global.pw.a2m.gz'.
make 1pht
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1pht' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1pht/1pht-T0099-local.pw -i /projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8327/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:        -55.816059
Database has 3 sequences with 224 residues.
gzip -f 1pht/1pht-T0099-local.pw.a2m
make 1pht
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1pht' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1pht/1pht-T0099-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8327/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:        -53.461720
Database has 3 sequences with 224 residues.
gzip -f 1pht/1pht-T0099-vit.pw.a2m
make 1pht
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1pht' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1pht/1pht-T0099-global.pw -i /projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pht/info/1pht.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pht/nostruct-align/1pht.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8327/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:        -50.693344
Database has 3 sequences with 224 residues.
gzip -f 1pht/1pht-T0099-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pht/xxxx-1pht-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1ckaA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make 1ckaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1ckaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/1ckaA-T0099-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26720/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:        -44.613525
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/1ckaA-T0099-local.pw.a2m
make 1ckaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1ckaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/1ckaA-T0099-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26720/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:        -41.877861
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/1ckaA-T0099-vit.pw.a2m
make 1ckaA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1ckaA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1ckaA/1ckaA-T0099-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckaA/info/1ckaA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1ckaA/nostruct-align/1ckaA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26720/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:        -40.869675
Database has 3 sequences with 170 residues.
gzip -f 1ckaA/1ckaA-T0099-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckaA/xxxx-1ckaA-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1bbzA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make 1bbzA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1bbzA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/1bbzA-T0099-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24277/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:        -43.682266
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/1bbzA-T0099-local.pw.a2m
make 1bbzA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1bbzA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/1bbzA-T0099-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24277/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:        -40.927929
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/1bbzA-T0099-vit.pw.a2m
make 1bbzA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1bbzA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1bbzA/1bbzA-T0099-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bbzA/info/1bbzA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bbzA/nostruct-align/1bbzA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24277/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:        -40.192333
Database has 3 sequences with 172 residues.
gzip -f 1bbzA/1bbzA-T0099-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bbzA/xxxx-1bbzA-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1bb9 PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make 1bb9
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1bb9' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/1bb9-T0099-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30369/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:        -56.193314
Database has 3 sequences with 254 residues.
gzip -f 1bb9/1bb9-T0099-local.pw.a2m
make 1bb9
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1bb9' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/1bb9-T0099-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30369/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:        -53.280315
Database has 3 sequences with 254 residues.
gzip -f 1bb9/1bb9-T0099-vit.pw.a2m
make 1bb9
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1bb9' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1bb9/1bb9-T0099-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bb9/info/1bb9.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bb9/nostruct-align/1bb9.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30369/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:        -50.224346
Database has 3 sequences with 254 residues.
gzip -f 1bb9/1bb9-T0099-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bb9/xxxx-1bb9-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1awj PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make 1awj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1awj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/1awj-T0099-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31603/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:        -49.914688
Database has 3 sequences with 210 residues.
gzip -f 1awj/1awj-T0099-local.pw.a2m
make 1awj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1awj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/1awj-T0099-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31603/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:        -47.233353
Database has 3 sequences with 210 residues.
gzip -f 1awj/1awj-T0099-vit.pw.a2m
make 1awj
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1awj' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1awj/1awj-T0099-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1awj/info/1awj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1awj/nostruct-align/1awj.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31603/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:        -45.485348
Database has 3 sequences with 210 residues.
gzip -f 1awj/1awj-T0099-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1awj/xxxx-1awj-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)
make -k PRED=1aojA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make 1aojA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1aojA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/1aojA-T0099-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30331/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:        -41.645000
Database has 3 sequences with 176 residues.
gzip -f 1aojA/1aojA-T0099-local.pw.a2m
make 1aojA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1aojA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/1aojA-T0099-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30331/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:        -38.712997
Database has 3 sequences with 176 residues.
gzip -f 1aojA/1aojA-T0099-vit.pw.a2m
make 1aojA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t99'
make[2]: `1aojA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
hmmscore 1aojA/1aojA-T0099-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod -db T0099.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aojA/info/1aojA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aojA/nostruct-align/1aojA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30331/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:        -38.553341
Database has 3 sequences with 176 residues.
gzip -f 1aojA/1aojA-T0099-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aojA/xxxx-1aojA-T0099-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t99'
make: [joints] Error 2 (ignored)