make -k PRED=1tum PRED2=1t joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
/projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.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/1t/1tum/struct-align/1tum.fssp.a2m.gz (2 sequences, 129 columns) as A2M alignment.
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
mkdir 1tum
fixmode 1tum
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.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:        -167.197021
Database has 2 sequences with 338 residues.
gzip -f 1tum/1tum-T0090-fssp-global.pw.a2m
/projects/compbio/experiments/models.97/scripts/w0.5 T0090.t2k.a2m.gz T0090.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 T0090.t2k.a2m.gz (126 sequences, 209 columns) as A2M alignment.
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/T0090-1tum-local.pw -i T0090.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k-w0.5.mod
T0090.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.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:        -143.273941
Database has 2 sequences with 338 residues.
gzip -f 1tum/T0090-1tum-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod', needed by `1tum/1tum-T0090-local.pw.a2m.gz'.
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/T0090-1tum-vit.pw \
	 -i T0090.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k-w0.5.mod
T0090.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.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:        -140.571426
Database has 2 sequences with 338 residues.
gzip -f 1tum/T0090-1tum-vit.pw.a2m
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/T0090-1tum-global.pw -i T0090.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k-w0.5.mod
T0090.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.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:        -210.677017
Database has 2 sequences with 338 residues.
gzip -f 1tum/T0090-1tum-global.pw.a2m
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod', needed by `1tum/1tum-T0090-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.noseed MODELNAME=noseed joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod', needed by `1tum/1tum-T0090-local.pw.a2m.gz'.
/projects/compbio/experiments/models.97/scripts/w0.5 T0090.t2k.noseed.a2m.gz T0090.t2k.noseed-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 T0090.t2k.noseed.a2m.gz (126 sequences, 136 columns) as A2M alignment.
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore -local.pw -i T0090.t2k.noseed-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.noseed-w0.5.mod
T0090.t2k.noseed-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.noseed.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:        -93.488922
Database has 2 sequences with 338 residues.
gzip -f -local.pw.a2m
gzip: illegal option -- o
usage: gzip [-cdfhlLnNrtvV19] [-S suffix] [file ...]
make[1]: *** [-local.pw.a2m.gz] Error 1
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.tuneup MODELNAME=tuneup joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod', needed by `1tum/1tum-T0090-local.pw.a2m.gz'.
/projects/compbio/experiments/models.97/scripts/w0.5 T0090.t2k.tuneup.a2m.gz T0090.t2k.tuneup-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 T0090.t2k.tuneup.a2m.gz (252 sequences, 165 columns) as A2M alignment.
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore -local.pw -i T0090.t2k.tuneup-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.tuneup-w0.5.mod
T0090.t2k.tuneup-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.tuneup.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:        -113.430435
Database has 2 sequences with 338 residues.
gzip -f -local.pw.a2m
gzip: illegal option -- o
usage: gzip [-cdfhlLnNrtvV19] [-S suffix] [file ...]
make[1]: *** [-local.pw.a2m.gz] Error 1
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
/projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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 /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k.a2m.gz (221 sequences, 129 columns) as A2M alignment.
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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:        -85.448441
Database has 2 sequences with 338 residues.
gzip -f 1tum/1tum-T0090-local.pw.a2m
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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:        -81.748932
Database has 2 sequences with 338 residues.
gzip -f 1tum/1tum-T0090-vit.pw.a2m
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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:        -139.292526
Database has 2 sequences with 338 residues.
gzip -f 1tum/1tum-T0090-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tum/xxxx-1tum-T0090-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.noseed MODELNAME=noseed joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/noseed-1tum-T0090-local.pw -i T0090.t2k.noseed-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.noseed-w0.5.mod
T0090.t2k.noseed-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.noseed.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:        -93.488922
Database has 2 sequences with 338 residues.
gzip -f 1tum/noseed-1tum-T0090-local.pw.a2m
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.tuneup MODELNAME=tuneup joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/tuneup-1tum-T0090-local.pw -i T0090.t2k.tuneup-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.tuneup-w0.5.mod
T0090.t2k.tuneup-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.tuneup.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:        -113.430435
Database has 2 sequences with 338 residues.
gzip -f 1tum/tuneup-1tum-T0090-local.pw.a2m
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make -k PRED=1tum PRED2=1t joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tum/xxxx-1tum-T0090-local.pw.a2m.gz'.
make[1]: *** No rule to make target `1tum/xxxx-1tum-T0090-global.pw.a2m.gz', needed by `joint'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.noseed MODELNAME=noseed joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `1tum/noseed-1tum-T0090-global.pw.a2m.gz', needed by `joint'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.tuneup MODELNAME=tuneup joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `1tum/tuneup-1tum-T0090-global.pw.a2m.gz', needed by `joint'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tum/xxxx-1tum-T0090-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.noseed MODELNAME=noseed joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/noseed-1tum-T0090-global.pw -i T0090.t2k.noseed-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.noseed-w0.5.mod
T0090.t2k.noseed-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.noseed.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:        -100.080536
Database has 2 sequences with 338 residues.
gzip -f 1tum/noseed-1tum-T0090-global.pw.a2m
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.tuneup MODELNAME=tuneup joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/tuneup-1tum-T0090-global.pw -i T0090.t2k.tuneup-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.tuneup-w0.5.mod
T0090.t2k.tuneup-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.tuneup.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:        -131.165512
Database has 2 sequences with 338 residues.
gzip -f 1tum/tuneup-1tum-T0090-global.pw.a2m
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t90'
make -k PRED=1tum PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/struct-align/1tum.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:        -199.167358
Database has 3 sequences with 467 residues.
gzip -f 1tum/1tum-T0090-fssp-global.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/T0090-1tum-local.pw -i T0090.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k-w0.5.mod
T0090.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.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:        -136.328033
Database has 3 sequences with 467 residues.
gzip -f 1tum/T0090-1tum-local.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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:        -97.044029
Database has 3 sequences with 467 residues.
gzip -f 1tum/1tum-T0090-local.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/T0090-1tum-vit.pw \
	-i T0090.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k-w0.5.mod
T0090.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.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:        -133.316025
Database has 3 sequences with 467 residues.
gzip -f 1tum/T0090-1tum-vit.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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:        -93.781029
Database has 3 sequences with 467 residues.
gzip -f 1tum/1tum-T0090-vit.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/T0090-1tum-global.pw -i T0090.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k-w0.5.mod
T0090.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.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:        -196.419357
Database has 3 sequences with 467 residues.
gzip -f 1tum/T0090-1tum-global.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/1tum-T0090-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tum/nostruct-align/1tum.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:        -151.148361
Database has 3 sequences with 467 residues.
gzip -f 1tum/1tum-T0090-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tum/xxxx-1tum-T0090-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
make: [joints] Error 2 (ignored)
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.noseed MODELNAME=noseed joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/noseed-1tum-T0090-local.pw -i T0090.t2k.noseed-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.noseed-w0.5.mod
T0090.t2k.noseed-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.noseed.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:        -96.937683
Database has 3 sequences with 467 residues.
gzip -f 1tum/noseed-1tum-T0090-local.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/noseed-1tum-T0090-global.pw -i T0090.t2k.noseed-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.noseed-w0.5.mod
T0090.t2k.noseed-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.noseed.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:        -102.523033
Database has 3 sequences with 467 residues.
gzip -f 1tum/noseed-1tum-T0090-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
make -k PRED=1tum PRED2=1t \
	MODELBASE=T0090.t2k.tuneup MODELNAME=tuneup joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/tuneup-1tum-T0090-local.pw -i T0090.t2k.tuneup-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.tuneup-w0.5.mod
T0090.t2k.tuneup-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.tuneup.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:        -113.752693
Database has 3 sequences with 467 residues.
gzip -f 1tum/tuneup-1tum-T0090-local.pw.a2m
make 1tum
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t90'
make[2]: `1tum' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'
hmmscore 1tum/tuneup-1tum-T0090-global.pw -i T0090.t2k.tuneup-w0.5.mod -db T0090.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tum/info/1tum.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0090.t2k.tuneup-w0.5.mod
T0090.t2k.tuneup-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0090.t2k.tuneup.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:        -129.697006
Database has 3 sequences with 467 residues.
gzip -f 1tum/tuneup-1tum-T0090-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t90'