make -k PRED=2ohxA PRED2=2o joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/2ohxA-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/struct-align/2ohxA.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2o/2ohxA/struct-align/2ohxA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2o/2ohxA/struct-align/2ohxA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/2o/2ohxA/struct-align/2ohxA.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:        -405.692719
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/2ohxA-T0087-fssp-global.pw.a2m
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/T0087-2ohxA-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -94.988953
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/T0087-2ohxA-local.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21361


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/tmp -alignfile /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k.a2m.gz (895 sequences, 374 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/tmp.a2m.
Dropping 25 (of 895) duplicate sequences with differing IDs
Dropping 566 (of 895) sequences with > 80.0% id
304 sequences left after dropping 591 of 895 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/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-21361/tmp.a2m (304 sequences, 374 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/tmp.mod /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21361 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/2ohxA-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/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:        -213.914001
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/2ohxA-T0087-local.pw.a2m
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/T0087-2ohxA-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -90.498940
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/T0087-2ohxA-vit.pw.a2m
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/2ohxA-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/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:        -209.728012
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/2ohxA-T0087-vit.pw.a2m
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/T0087-2ohxA-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -225.092407
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/T0087-2ohxA-global.pw.a2m
make 2ohxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `2ohxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 2ohxA/2ohxA-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2o/2ohxA/info/2ohxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/2o/2ohxA/nostruct-align/2ohxA.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21361/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:        -349.197418
Database has 3 sequences with 1058 residues.
gzip -f 2ohxA/2ohxA-T0087-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2ohxA/xxxx-2ohxA-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1pjr PRED2=1p joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/1pjr-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1p/1pjr/struct-align/1pjr.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pjr/struct-align/1pjr.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pjr/struct-align/1pjr.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1p/1pjr/struct-align/1pjr.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:        -700.183777
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/1pjr-T0087-fssp-global.pw.a2m
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/T0087-1pjr-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -97.079811
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/T0087-1pjr-local.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-570


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-570/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k.a2m.gz (129 sequences, 623 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-570/tmp.a2m.
Dropping 1 (of 129) duplicate sequences with differing IDs
Dropping 39 (of 129) sequences with > 80.0% id
89 sequences left after dropping 40 of 129 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-570/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-570/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-570/tmp.a2m (89 sequences, 623 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-570/tmp.mod /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-570 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/1pjr-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-570/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:        -369.581055
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/1pjr-T0087-local.pw.a2m
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/T0087-1pjr-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -90.672813
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/T0087-1pjr-vit.pw.a2m
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/1pjr-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-570/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:        -364.585785
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/1pjr-T0087-vit.pw.a2m
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/T0087-1pjr-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -313.651001
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/T0087-1pjr-global.pw.a2m
make 1pjr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1pjr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1pjr/1pjr-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1p/1pjr/info/1pjr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1p/1pjr/nostruct-align/1pjr.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-570/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:        -588.240051
Database has 3 sequences with 1657 residues.
gzip -f 1pjr/1pjr-T0087-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pjr/xxxx-1pjr-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1tbgE PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/1tbgE-T0087-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tbgE/struct-align/1tbgE.fssp-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tbgE/struct-align/1tbgE.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tbgE/struct-align/1tbgE.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/experiments/models.97/pdb/1t/1tbgE/struct-align/1tbgE.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:        -121.880714
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/1tbgE-T0087-fssp-global.pw.a2m
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/T0087-1tbgE-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -94.950172
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/T0087-1tbgE-local.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27627


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k.a2m.gz (69 sequences, 68 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/tmp.a2m.
Dropping 12 (of 69) duplicate sequences with differing IDs
Dropping 35 (of 69) sequences with > 80.0% id
22 sequences left after dropping 47 of 69 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/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-27627/tmp.a2m (22 sequences, 68 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/tmp.mod /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27627 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/1tbgE-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -43.938496
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/1tbgE-T0087-local.pw.a2m
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/T0087-1tbgE-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -90.312157
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/T0087-1tbgE-vit.pw.a2m
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/1tbgE-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -40.646168
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/1tbgE-T0087-vit.pw.a2m
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/T0087-1tbgE-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.t2k.a2m.gz
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -129.908371
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/T0087-1tbgE-global.pw.a2m
make 1tbgE
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1tbgE' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1tbgE/1tbgE-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tbgE/info/1tbgE.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tbgE/nostruct-align/1tbgE.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27627/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:        -83.699699
Database has 3 sequences with 446 residues.
gzip -f 1tbgE/1tbgE-T0087-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tbgE/xxxx-1tbgE-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)
make -k PRED=1qhgB PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qhgB/struct-align/1qhgB.fssp-w0.5.mod', needed by `1qhgB/1qhgB-T0087-fssp-global.pw.a2m.gz'.
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1qhgB/T0087-1qhgB-local.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -97.404846
Database has 3 sequences with 844 residues.
gzip -f 1qhgB/T0087-1qhgB-local.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20914


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k.a2m.gz (99 sequences, 261 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/tmp.a2m.
Dropping 8 (of 99) duplicate sequences with differing IDs
Dropping 21 (of 99) sequences with > 80.0% id
70 sequences left after dropping 29 of 99 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/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-20914/tmp.a2m (70 sequences, 261 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20914 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1qhgB/1qhgB-T0087-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -164.679855
Database has 3 sequences with 844 residues.
gzip -f 1qhgB/1qhgB-T0087-local.pw.a2m
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1qhgB/T0087-1qhgB-vit.pw \
	-i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -91.287842
Database has 3 sequences with 844 residues.
gzip -f 1qhgB/T0087-1qhgB-vit.pw.a2m
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1qhgB/1qhgB-T0087-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/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:        -161.379166
Database has 3 sequences with 844 residues.
gzip -f 1qhgB/1qhgB-T0087-vit.pw.a2m
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1qhgB/T0087-1qhgB-global.pw -i T0087.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0087.t2k-w0.5.mod
T0087.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file T0087.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:        -201.652054
Database has 3 sequences with 844 residues.
gzip -f 1qhgB/T0087-1qhgB-global.pw.a2m
make 1qhgB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t87'
make[2]: `1qhgB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
hmmscore 1qhgB/1qhgB-T0087-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod -db T0087.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qhgB/info/1qhgB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qhgB/nostruct-align/1qhgB.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20914/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:        -273.078033
Database has 3 sequences with 844 residues.
gzip -f 1qhgB/1qhgB-T0087-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhgB/xxxx-1qhgB-T0087-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87'
make: [joints] Error 2 (ignored)