make -k PRED=1cov3 PRED2=1c joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cov3/struct-align/1cov3.fssp-w0.5.mod', needed by `1cov3/1cov3-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cov3/nostruct-align/1cov3.t2k-w0.5.mod', needed by `1cov3/1cov3-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cov3/xxxx-1cov3-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1aym3 PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t2k-w0.5.mod', needed by `1aym3/1aym3-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aym3/xxxx-1aym3-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bn8A PRED2=1b joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/struct-align/1bn8A.fssp-w0.5.mod', needed by `1bn8A/1bn8A-T0100-fssp-global.pw.a2m.gz'.
make 1bn8A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
mkdir 1bn8A
fixmode 1bn8A
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 1bn8A/T0100-1bn8A-local.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -100.645668
Database has 3 sequences with 1161 residues.
gzip -f 1bn8A/T0100-1bn8A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t2k-w0.5.mod', needed by `1bn8A/1bn8A-T0100-local.pw.a2m.gz'.
make 1bn8A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `1bn8A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 1bn8A/T0100-1bn8A-vit.pw \
	-i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -95.239685
Database has 3 sequences with 1161 residues.
gzip -f 1bn8A/T0100-1bn8A-vit.pw.a2m
make 1bn8A
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `1bn8A' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 1bn8A/T0100-1bn8A-global.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -238.755997
Database has 3 sequences with 1161 residues.
gzip -f 1bn8A/T0100-1bn8A-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bn8A/xxxx-1bn8A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bn8A PRED2=1b joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/struct-align/1bn8A.fssp-w0.5.mod', needed by `1bn8A/1bn8A-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t2k-w0.5.mod', needed by `1bn8A/1bn8A-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bn8A/xxxx-1bn8A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1aqm PRED2=1a joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aqm/struct-align/1aqm.fssp-w0.5.mod', needed by `1aqm/1aqm-T0100-fssp-global.pw.a2m.gz'.
make 1aqm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
mkdir 1aqm
fixmode 1aqm
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 1aqm/T0100-1aqm-local.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -102.389931
Database has 3 sequences with 1243 residues.
gzip -f 1aqm/T0100-1aqm-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t2k-w0.5.mod', needed by `1aqm/1aqm-T0100-local.pw.a2m.gz'.
make 1aqm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `1aqm' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 1aqm/T0100-1aqm-vit.pw \
	-i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -94.666603
Database has 3 sequences with 1243 residues.
gzip -f 1aqm/T0100-1aqm-vit.pw.a2m
make 1aqm
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `1aqm' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 1aqm/T0100-1aqm-global.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -248.277405
Database has 3 sequences with 1243 residues.
gzip -f 1aqm/T0100-1aqm-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aqm/xxxx-1aqm-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=2qwc PRED2=2q joint
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-19600


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-19600/tmp -alignfile /projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.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/2q/2qwc/struct-align/2qwc.fssp.a2m.gz (71 sequences, 388 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-19600/tmp.a2m.
Dropping 41 (of 71) duplicate sequences with differing IDs
Dropping 16 (of 71) sequences with > 80.0% id
14 sequences left after dropping 57 of 71 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-19600/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-19600/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-purr-19600/tmp.a2m (14 sequences, 388 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-19600/tmp.mod /projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-purr-19600 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 2qwc
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
mkdir 2qwc
fixmode 2qwc
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/2qwc-T0100-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.fssp-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2q/2qwc/struct-align/2qwc.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-19600/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:        -213.936722
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/2qwc-T0100-fssp-global.pw.a2m
make 2qwc
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `2qwc' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/T0100-2qwc-local.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -100.815392
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/T0100-2qwc-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t2k-w0.5.mod', needed by `2qwc/2qwc-T0100-local.pw.a2m.gz'.
make 2qwc
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `2qwc' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/T0100-2qwc-vit.pw \
	-i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -93.178734
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/T0100-2qwc-vit.pw.a2m
make 2qwc
make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t100'
make[2]: `2qwc' is up to date.
make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/T0100-2qwc-global.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -240.506653
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/T0100-2qwc-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2qwc/xxxx-2qwc-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1cov3 PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cov3/struct-align/1cov3.fssp-w0.5.mod', needed by `1cov3/1cov3-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cov3/nostruct-align/1cov3.t2k-w0.5.mod', needed by `1cov3/1cov3-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cov3/xxxx-1cov3-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1aym3 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t2k-w0.5.mod', needed by `1aym3/1aym3-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aym3/xxxx-1aym3-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bn8A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/struct-align/1bn8A.fssp-w0.5.mod', needed by `1bn8A/1bn8A-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t2k-w0.5.mod', needed by `1bn8A/1bn8A-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bn8A/xxxx-1bn8A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bn8A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/struct-align/1bn8A.fssp-w0.5.mod', needed by `1bn8A/1bn8A-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t2k-w0.5.mod', needed by `1bn8A/1bn8A-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bn8A/xxxx-1bn8A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1aqm PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aqm/struct-align/1aqm.fssp-w0.5.mod', needed by `1aqm/1aqm-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t2k-w0.5.mod', needed by `1aqm/1aqm-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aqm/xxxx-1aqm-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=2qwc PRED2=2q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t2k-w0.5.mod', needed by `2qwc/2qwc-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2qwc/xxxx-2qwc-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t2k-w0.5.mod', needed by `1dbgA/1dbgA-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t2k-w0.5.mod', needed by `1rmg/1rmg-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t2k-w0.5.mod', needed by `1bhe/1bhe-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t2k-w0.5.mod', needed by `1czfA/1czfA-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t2k-w0.5.mod', needed by `1air/1air-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t2k-w0.5.mod', needed by `1qa1A/1qa1A-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t2k-w0.5.mod', needed by `1qcxA/1qcxA-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t2k-w0.5.mod', needed by `1dabA/1dabA-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t2k-w0.5.mod', needed by `1tyv/1tyv-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1ex1A  PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26837


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26837/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.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/1e/1ex1A/struct-align/1ex1A.fssp.a2m.gz (35 sequences, 602 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26837/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26837/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26837/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-26837/tmp.a2m (35 sequences, 602 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26837/tmp.mod /projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26837 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
mkdir 1ex1A
fixmode 1ex1A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/1ex1A-T0100-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.fssp-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1ex1A/struct-align/1ex1A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26837/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:        -260.288055
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/1ex1A-T0100-fssp-global.pw.a2m
make 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1ex1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/T0100-1ex1A-local.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -103.787964
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/T0100-1ex1A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t2k-w0.5.mod', needed by `1ex1A/1ex1A-T0100-local.pw.a2m.gz'.
make 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1ex1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/T0100-1ex1A-vit.pw \
	-i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -96.348938
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/T0100-1ex1A-vit.pw.a2m
make 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1ex1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/T0100-1ex1A-global.pw -i T0100.t2k-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0100.t2k-w0.5.mod
T0100.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-18575/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:        -279.962708
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/T0100-1ex1A-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ex1A/xxxx-1ex1A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1cov3 PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cov3/struct-align/1cov3.fssp-w0.5.mod', needed by `1cov3/1cov3-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cov3/nostruct-align/1cov3.t99-w0.5.mod', needed by `1cov3/1cov3-T0100-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cov3/xxxx-1cov3-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1aym3 PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1aym3
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1aym3' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1aym3/1aym3-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aym3/info/1aym3.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aym3/info/1aym3.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4505/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:        -143.339249
Database has 3 sequences with 818 residues.
gzip -f 1aym3/1aym3-T0100-local.pw.a2m
make 1aym3
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1aym3' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1aym3/1aym3-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aym3/info/1aym3.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aym3/info/1aym3.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4505/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:        -139.483566
Database has 3 sequences with 818 residues.
gzip -f 1aym3/1aym3-T0100-vit.pw.a2m
make 1aym3
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1aym3' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1aym3/1aym3-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aym3/info/1aym3.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aym3/info/1aym3.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aym3/nostruct-align/1aym3.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4505/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:        -134.514389
Database has 3 sequences with 818 residues.
gzip -f 1aym3/1aym3-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aym3/xxxx-1aym3-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bn8A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/struct-align/1bn8A.fssp-w0.5.mod', needed by `1bn8A/1bn8A-T0100-fssp-global.pw.a2m.gz'.
make 1bn8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1bn8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1bn8A/1bn8A-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6765/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:        -222.131027
Database has 3 sequences with 1161 residues.
gzip -f 1bn8A/1bn8A-T0100-local.pw.a2m
make 1bn8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1bn8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1bn8A/1bn8A-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6765/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -216.988708
Database has 3 sequences with 1161 residues.
gzip -f 1bn8A/1bn8A-T0100-vit.pw.a2m
make 1bn8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1bn8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1bn8A/1bn8A-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bn8A/info/1bn8A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bn8A/nostruct-align/1bn8A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6765/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:        -215.965042
Database has 3 sequences with 1161 residues.
gzip -f 1bn8A/1bn8A-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bn8A/xxxx-1bn8A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bn8A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bn8A/struct-align/1bn8A.fssp-w0.5.mod', needed by `1bn8A/1bn8A-T0100-fssp-global.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bn8A/xxxx-1bn8A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1aqm PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aqm/struct-align/1aqm.fssp-w0.5.mod', needed by `1aqm/1aqm-T0100-fssp-global.pw.a2m.gz'.
make 1aqm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1aqm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1aqm/1aqm-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29488/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -240.419617
Database has 3 sequences with 1243 residues.
gzip -f 1aqm/1aqm-T0100-local.pw.a2m
make 1aqm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1aqm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1aqm/1aqm-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29488/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:        -235.805954
Database has 3 sequences with 1243 residues.
gzip -f 1aqm/1aqm-T0100-vit.pw.a2m
make 1aqm
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1aqm' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1aqm/1aqm-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aqm/info/1aqm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aqm/nostruct-align/1aqm.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29488/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:        -223.066757
Database has 3 sequences with 1243 residues.
gzip -f 1aqm/1aqm-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aqm/xxxx-1aqm-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=2qwc PRED2=2q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 2qwc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `2qwc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/2qwc-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11845/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:        -315.226410
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/2qwc-T0100-local.pw.a2m
make 2qwc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `2qwc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/2qwc-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11845/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:        -311.697083
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/2qwc-T0100-vit.pw.a2m
make 2qwc
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `2qwc' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 2qwc/2qwc-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2q/2qwc/info/2qwc.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2q/2qwc/nostruct-align/2qwc.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11845/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:        -308.484009
Database has 3 sequences with 1118 residues.
gzip -f 2qwc/2qwc-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2qwc/xxxx-2qwc-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1dbgA/1dbgA-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7413/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:        -380.104980
Database has 3 sequences with 1329 residues.
gzip -f 1dbgA/1dbgA-T0100-local.pw.a2m
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1dbgA/1dbgA-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7413/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:        -376.186646
Database has 3 sequences with 1329 residues.
gzip -f 1dbgA/1dbgA-T0100-vit.pw.a2m
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1dbgA/1dbgA-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7413/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:        -375.605377
Database has 3 sequences with 1329 residues.
gzip -f 1dbgA/1dbgA-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1rmg/1rmg-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14068/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -223.061401
Database has 3 sequences with 1186 residues.
gzip -f 1rmg/1rmg-T0100-local.pw.a2m
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1rmg/1rmg-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14068/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:        -217.787399
Database has 3 sequences with 1186 residues.
gzip -f 1rmg/1rmg-T0100-vit.pw.a2m
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1rmg/1rmg-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14068/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:        -232.423401
Database has 3 sequences with 1186 residues.
gzip -f 1rmg/1rmg-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1bhe/1bhe-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4921/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -177.184036
Database has 3 sequences with 1094 residues.
gzip -f 1bhe/1bhe-T0100-local.pw.a2m
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1bhe/1bhe-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4921/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:        -171.070419
Database has 3 sequences with 1094 residues.
gzip -f 1bhe/1bhe-T0100-vit.pw.a2m
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1bhe/1bhe-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4921/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:        -179.067734
Database has 3 sequences with 1094 residues.
gzip -f 1bhe/1bhe-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1czfA/1czfA-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12403/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:        -200.095871
Database has 3 sequences with 1039 residues.
gzip -f 1czfA/1czfA-T0100-local.pw.a2m
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1czfA/1czfA-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12403/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:        -196.211533
Database has 3 sequences with 1039 residues.
gzip -f 1czfA/1czfA-T0100-vit.pw.a2m
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1czfA/1czfA-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12403/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:        -193.608047
Database has 3 sequences with 1039 residues.
gzip -f 1czfA/1czfA-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1air/1air-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-937/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:        -193.474426
Database has 3 sequences with 1047 residues.
gzip -f 1air/1air-T0100-local.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1air/1air-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-937/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:        -189.933060
Database has 3 sequences with 1047 residues.
gzip -f 1air/1air-T0100-vit.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1air/1air-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-937/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:        -188.461380
Database has 3 sequences with 1047 residues.
gzip -f 1air/1air-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1qa1A/1qa1A-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31080/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:        -575.101990
Database has 3 sequences with 1438 residues.
gzip -f 1qa1A/1qa1A-T0100-local.pw.a2m
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1qa1A/1qa1A-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31080/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:        -572.260681
Database has 3 sequences with 1438 residues.
gzip -f 1qa1A/1qa1A-T0100-vit.pw.a2m
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1qa1A/1qa1A-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31080/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:        -771.879700
Database has 3 sequences with 1438 residues.
gzip -f 1qa1A/1qa1A-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1qcxA/1qcxA-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20881/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:        -205.396606
Database has 3 sequences with 1060 residues.
gzip -f 1qcxA/1qcxA-T0100-local.pw.a2m
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1qcxA/1qcxA-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20881/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:        -200.284592
Database has 3 sequences with 1060 residues.
gzip -f 1qcxA/1qcxA-T0100-vit.pw.a2m
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1qcxA/1qcxA-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20881/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:        -202.329391
Database has 3 sequences with 1060 residues.
gzip -f 1qcxA/1qcxA-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1dabA/1dabA-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1167/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:        -273.504608
Database has 3 sequences with 1420 residues.
gzip -f 1dabA/1dabA-T0100-local.pw.a2m
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1dabA/1dabA-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1167/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:        -266.758972
Database has 3 sequences with 1420 residues.
gzip -f 1dabA/1dabA-T0100-vit.pw.a2m
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1dabA/1dabA-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1167/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:        -256.092377
Database has 3 sequences with 1420 residues.
gzip -f 1dabA/1dabA-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1tyv/1tyv-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22469/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:        -577.846985
Database has 3 sequences with 1426 residues.
gzip -f 1tyv/1tyv-T0100-local.pw.a2m
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1tyv/1tyv-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22469/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:        -575.042969
Database has 3 sequences with 1426 residues.
gzip -f 1tyv/1tyv-T0100-vit.pw.a2m
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1tyv/1tyv-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22469/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:        -772.815002
Database has 3 sequences with 1426 residues.
gzip -f 1tyv/1tyv-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)
make -k PRED=1ex1A  PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1ex1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/1ex1A-T0100-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24094/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:        -336.596954
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/1ex1A-T0100-local.pw.a2m
make 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1ex1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/1ex1A-T0100-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24094/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:        -332.158234
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/1ex1A-T0100-vit.pw.a2m
make 1ex1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t100'
make[2]: `1ex1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
hmmscore 1ex1A/1ex1A-T0100-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod -db T0100.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1ex1A/info/1ex1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1e/1ex1A/nostruct-align/1ex1A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24094/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -325.669403
Database has 3 sequences with 1549 residues.
gzip -f 1ex1A/1ex1A-T0100-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ex1A/xxxx-1ex1A-T0100-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100'
make: [joints] Error 2 (ignored)