make -k PRED=1nseA PRED2=1n joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.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/1n/1nseA/struct-align/1nseA.fssp.a2m.gz (42 sequences, 416 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704/tmp.a2m.
Dropping 26 (of 42) duplicate sequences with differing IDs
Dropping 14 (of 42) sequences with > 80.0% id
2 sequences left after dropping 40 of 42 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704/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-eclipse-4704/tmp.a2m (2 sequences, 416 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704/tmp.mod /projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1nseA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
mkdir 1nseA
fixmode 1nseA
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1nseA/1nseA-T0098-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.fssp-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1n/1nseA/struct-align/1nseA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4704/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:        -540.554749
Database has 3 sequences with 981 residues.
gzip -f 1nseA/1nseA-T0098-fssp-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 T0098.t2k.a2m.gz T0098.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp -alignfile T0098.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 T0098.t2k.a2m.gz (36 sequences, 121 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m.
Dropping 2 (of 36) duplicate sequences with differing IDs
Dropping 27 (of 36) sequences with > 80.0% id
7 sequences left after dropping 29 of 36 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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-eclipse-9049/tmp.a2m (7 sequences, 121 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.mod T0098.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1nseA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1nseA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1nseA/T0098-1nseA-local.pw -i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -59.654980
Database has 3 sequences with 981 residues.
gzip -f 1nseA/T0098-1nseA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t2k-w0.5.mod', needed by `1nseA/1nseA-T0098-local.pw.a2m.gz'.
make 1nseA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1nseA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1nseA/T0098-1nseA-vit.pw \
	-i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -55.710621
Database has 3 sequences with 981 residues.
gzip -f 1nseA/T0098-1nseA-vit.pw.a2m
make 1nseA
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1nseA' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1nseA/T0098-1nseA-global.pw -i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -137.943375
Database has 3 sequences with 981 residues.
gzip -f 1nseA/T0098-1nseA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
make: [joints] Error 2 (ignored)
make -k PRED=1bxm PRED2=1b joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.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/1bxm/struct-align/1bxm.fssp.a2m.gz (3 sequences, 99 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820/tmp.a2m.
Dropping 2 (of 3) sequences with > 80.0% id
1 sequences left after dropping 2 of 3 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820/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-eclipse-7820/tmp.a2m (1 sequences, 99 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1bxm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
mkdir 1bxm
fixmode 1bxm
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1bxm/1bxm-T0098-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.fssp-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bxm/struct-align/1bxm.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7820/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:        -148.612686
Database has 3 sequences with 319 residues.
gzip -f 1bxm/1bxm-T0098-fssp-global.pw.a2m
make 1bxm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1bxm' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1bxm/T0098-1bxm-local.pw -i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -60.641674
Database has 3 sequences with 319 residues.
gzip -f 1bxm/T0098-1bxm-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t2k-w0.5.mod', needed by `1bxm/1bxm-T0098-local.pw.a2m.gz'.
make 1bxm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1bxm' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1bxm/T0098-1bxm-vit.pw \
	-i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -57.210663
Database has 3 sequences with 319 residues.
gzip -f 1bxm/T0098-1bxm-vit.pw.a2m
make 1bxm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1bxm' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1bxm/T0098-1bxm-global.pw -i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -90.879028
Database has 3 sequences with 319 residues.
gzip -f 1bxm/T0098-1bxm-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
make: [joints] Error 2 (ignored)
make -k PRED=1au7A PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.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/1au7A/struct-align/1au7A.fssp.a2m.gz (11 sequences, 130 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106/tmp.a2m.
Dropping 3 (of 11) sequences with > 80.0% id
8 sequences left after dropping 3 of 11 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106/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-eclipse-25106/tmp.a2m (8 sequences, 130 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1au7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
mkdir 1au7A
fixmode 1au7A
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1au7A/1au7A-T0098-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.fssp-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1au7A/struct-align/1au7A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-25106/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:        -150.040359
Database has 3 sequences with 397 residues.
gzip -f 1au7A/1au7A-T0098-fssp-global.pw.a2m
make 1au7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1au7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1au7A/T0098-1au7A-local.pw -i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -59.829712
Database has 3 sequences with 397 residues.
gzip -f 1au7A/T0098-1au7A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t2k-w0.5.mod', needed by `1au7A/1au7A-T0098-local.pw.a2m.gz'.
make 1au7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1au7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1au7A/T0098-1au7A-vit.pw \
	-i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -54.698383
Database has 3 sequences with 397 residues.
gzip -f 1au7A/T0098-1au7A-vit.pw.a2m
make 1au7A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t98'
make[2]: `1au7A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
hmmscore 1au7A/T0098-1au7A-global.pw -i T0098.t2k-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0098.t2k-w0.5.mod
T0098.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/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:        -103.863350
Database has 3 sequences with 397 residues.
gzip -f 1au7A/T0098-1au7A-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98'
make: [joints] Error 2 (ignored)