make -k PRED=1a12A PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t88'
/projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod
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/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp.a2m.gz (14 sequences, 401 columns) as A2M alignment.
make 1a12A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t88'
mkdir 1a12A
fixmode 1a12A
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 04/18/00_11:44:03
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:        -230.844589
Database has 2 sequences with 569 residues.
gzip -f 1a12A/1a12A-T0088-fssp-global.pw.a2m
/projects/compbio/experiments/models.97/scripts/w0.5 T0088.t2k.a2m.gz T0088.t2k-w0.5.mod
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 T0088.t2k.a2m.gz (10 sequences, 156 columns) as A2M alignment.
make 1a12A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/T0088-1a12A-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 04/18/00_11:44:03
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -130.928925
Database has 2 sequences with 569 residues.
gzip -f 1a12A/T0088-1a12A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod', needed by `1a12A/1a12A-T0088-local.pw.a2m.gz'.
make 1a12A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/T0088-1a12A-vit.pw \
	 -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 04/18/00_11:44:03
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -127.177887
Database has 2 sequences with 569 residues.
gzip -f 1a12A/T0088-1a12A-vit.pw.a2m
make 1a12A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/T0088-1a12A-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 04/18/00_11:44:03
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:        -210.872070
Database has 2 sequences with 569 residues.
gzip -f 1a12A/T0088-1a12A-global.pw.a2m
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)
make -k PRED=1a12A PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13511


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.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 /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k.a2m.gz (86 sequences, 401 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/tmp.a2m.
Dropping 7 (of 86) duplicate sequences with differing IDs
Dropping 19 (of 86) sequences with > 80.0% id
60 sequences left after dropping 26 of 86 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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-13511/tmp.a2m (60 sequences, 401 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13511 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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:        -169.105377
Database has 2 sequences with 569 residues.
gzip -f 1a12A/1a12A-T0088-local.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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:        -164.012894
Database has 2 sequences with 569 residues.
gzip -f 1a12A/1a12A-T0088-vit.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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:        -226.174561
Database has 2 sequences with 569 residues.
gzip -f 1a12A/1a12A-T0088-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a12A/xxxx-1a12A-T0088-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)
make -k PRED=1led PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19222


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.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/1l/1led/struct-align/1led.fssp.a2m.gz (132 sequences, 243 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/tmp.a2m.
Dropping 88 (of 132) duplicate sequences with differing IDs
Dropping 20 (of 132) sequences with > 80.0% id
24 sequences left after dropping 108 of 132 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/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-19222/tmp.a2m (24 sequences, 243 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/tmp.mod /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19222 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
mkdir 1led
fixmode 1led
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/1led-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/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:        -117.943527
Database has 2 sequences with 400 residues.
gzip -f 1led/1led-T0088-fssp-global.pw.a2m
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/T0088-1led-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -127.334511
Database has 2 sequences with 400 residues.
gzip -f 1led/T0088-1led-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1l/1led/nostruct-align/1led.t2k-w0.5.mod', needed by `1led/1led-T0088-local.pw.a2m.gz'.
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/T0088-1led-vit.pw \
	 -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -123.084503
Database has 2 sequences with 400 residues.
gzip -f 1led/T0088-1led-vit.pw.a2m
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/T0088-1led-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
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:        -195.321014
Database has 2 sequences with 400 residues.
gzip -f 1led/T0088-1led-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1led/xxxx-1led-T0088-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)
make -k PRED=1wkt PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-564


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-564/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.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/1w/1wkt/struct-align/1wkt.fssp.a2m.gz (1 sequences, 87 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-564/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-564/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-564/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-564/tmp.a2m (1 sequences, 87 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-564/tmp.mod /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-564 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
mkdir 1wkt
fixmode 1wkt
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/1wkt-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-564/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:        -122.518021
Database has 2 sequences with 244 residues.
gzip -f 1wkt/1wkt-T0088-fssp-global.pw.a2m
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/T0088-1wkt-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -130.434906
Database has 2 sequences with 244 residues.
gzip -f 1wkt/T0088-1wkt-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1w/1wkt/nostruct-align/1wkt.t2k-w0.5.mod', needed by `1wkt/1wkt-T0088-local.pw.a2m.gz'.
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/T0088-1wkt-vit.pw \
	 -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -125.886414
Database has 2 sequences with 244 residues.
gzip -f 1wkt/T0088-1wkt-vit.pw.a2m
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/T0088-1wkt-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
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:        -175.870026
Database has 2 sequences with 244 residues.
gzip -f 1wkt/T0088-1wkt-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wkt/xxxx-1wkt-T0088-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)
make -k PRED=1a12A PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1a12A/struct-align/1a12A.fssp.a2m.gz
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:        -316.989746
Database has 3 sequences with 970 residues.
gzip -f 1a12A/1a12A-T0088-fssp-global.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/T0088-1a12A-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -92.700623
Database has 3 sequences with 970 residues.
gzip -f 1a12A/T0088-1a12A-local.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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:        -221.557602
Database has 3 sequences with 970 residues.
gzip -f 1a12A/1a12A-T0088-local.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/T0088-1a12A-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -88.131935
Database has 3 sequences with 970 residues.
gzip -f 1a12A/T0088-1a12A-vit.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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:        -217.032272
Database has 3 sequences with 970 residues.
gzip -f 1a12A/1a12A-T0088-vit.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/T0088-1a12A-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
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:        -175.290085
Database has 3 sequences with 970 residues.
gzip -f 1a12A/T0088-1a12A-global.pw.a2m
make 1a12A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1a12A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1a12A/1a12A-T0088-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a12A/info/1a12A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a12A/nostruct-align/1a12A.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13511/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:        -295.427399
Database has 3 sequences with 970 residues.
gzip -f 1a12A/1a12A-T0088-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a12A/xxxx-1a12A-T0088-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)
make -k PRED=1led PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/1led-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1led/struct-align/1led.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19222/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:        -152.791031
Database has 3 sequences with 643 residues.
gzip -f 1led/1led-T0088-fssp-global.pw.a2m
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/T0088-1led-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -87.896996
Database has 3 sequences with 643 residues.
gzip -f 1led/T0088-1led-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1l/1led/nostruct-align/1led.t2k-w0.5.mod', needed by `1led/1led-T0088-local.pw.a2m.gz'.
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/T0088-1led-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -82.665672
Database has 3 sequences with 643 residues.
gzip -f 1led/T0088-1led-vit.pw.a2m
make 1led
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1led' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1led/T0088-1led-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1led/info/1led.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
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:        -154.708679
Database has 3 sequences with 643 residues.
gzip -f 1led/T0088-1led-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1led/xxxx-1led-T0088-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)
make -k PRED=1wkt PRED2=1w joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/1wkt-T0088-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1w/1wkt/struct-align/1wkt.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-564/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:        -145.159683
Database has 3 sequences with 332 residues.
gzip -f 1wkt/1wkt-T0088-fssp-global.pw.a2m
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/T0088-1wkt-local.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -92.032166
Database has 3 sequences with 332 residues.
gzip -f 1wkt/T0088-1wkt-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1w/1wkt/nostruct-align/1wkt.t2k-w0.5.mod', needed by `1wkt/1wkt-T0088-local.pw.a2m.gz'.
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/T0088-1wkt-vit.pw \
	-i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -86.400169
Database has 3 sequences with 332 residues.
gzip -f 1wkt/T0088-1wkt-vit.pw.a2m
make 1wkt
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t88'
make[2]: `1wkt' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
hmmscore 1wkt/T0088-1wkt-global.pw -i T0088.t2k-w0.5.mod -db T0088.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1w/1wkt/info/1wkt.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0088.t2k-w0.5.mod
T0088.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0088.t2k.a2m.gz
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:        -129.380692
Database has 3 sequences with 332 residues.
gzip -f 1wkt/T0088-1wkt-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wkt/xxxx-1wkt-T0088-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t88'
make: [joints] Error 2 (ignored)