make -k PRED=1qaaA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qaaA/struct-align/1qaaA.fssp-w0.5.mod', needed by `1qaaA/1qaaA-T0096-fssp-global.pw.a2m.gz'.
/projects/compbio/bin/scripts/w0.5 T0096.t2k.a2m.gz T0096.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25261


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp -alignfile T0096.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 T0096.t2k.a2m.gz (115 sequences, 239 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp.a2m.
Dropping 6 (of 115) duplicate sequences with differing IDs
Dropping 13 (of 115) sequences with > 80.0% id
96 sequences left after dropping 19 of 115 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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-25261/tmp.a2m (96 sequences, 239 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp.mod T0096.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25261 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qaaA/info/1qaaA.stride-mixed.seq', needed by `1qaaA/T0096-1qaaA-local.pw.a2m.gz'.
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qaaA/nostruct-align/1qaaA.t2k-w0.5.mod', needed by `1qaaA/1qaaA-T0096-local.pw.a2m.gz'.
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qaaA/xxxx-1qaaA-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1lea PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11878


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp.a2m.gz (6 sequences, 72 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/tmp.a2m.
Dropping 1 (of 6) duplicate sequences with differing IDs
5 sequences left after dropping 1 of 6 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/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-11878/tmp.a2m (5 sequences, 72 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/tmp.mod /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11878 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 1lea
fixmode 1lea
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/1lea-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/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:        -34.276001
Database has 2 sequences with 323 residues.
gzip -f 1lea/1lea-T0096-fssp-global.pw.a2m
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/T0096-1lea-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -91.242401
Database has 2 sequences with 323 residues.
gzip -f 1lea/T0096-1lea-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1l/1lea/nostruct-align/1lea.t2k-w0.5.mod', needed by `1lea/1lea-T0096-local.pw.a2m.gz'.
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/T0096-1lea-vit.pw \
	 -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -87.109406
Database has 2 sequences with 323 residues.
gzip -f 1lea/T0096-1lea-vit.pw.a2m
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/T0096-1lea-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -154.391510
Database has 2 sequences with 323 residues.
gzip -f 1lea/T0096-1lea-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lea/xxxx-1lea-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1bia PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23376


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp.a2m.gz (7 sequences, 292 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/tmp.a2m.
Dropping 1 (of 7) sequences with > 80.0% id
6 sequences left after dropping 1 of 7 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/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-23376/tmp.a2m (6 sequences, 292 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23376 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 1bia
fixmode 1bia
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/1bia-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -152.080017
Database has 2 sequences with 560 residues.
gzip -f 1bia/1bia-T0096-fssp-global.pw.a2m
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/T0096-1bia-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -91.100616
Database has 2 sequences with 560 residues.
gzip -f 1bia/T0096-1bia-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bia/nostruct-align/1bia.t2k-w0.5.mod', needed by `1bia/1bia-T0096-local.pw.a2m.gz'.
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/T0096-1bia-vit.pw \
	 -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -86.251617
Database has 2 sequences with 560 residues.
gzip -f 1bia/T0096-1bia-vit.pw.a2m
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/T0096-1bia-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -193.485077
Database has 2 sequences with 560 residues.
gzip -f 1bia/T0096-1bia-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bia/xxxx-1bia-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=2cgpA PRED2=2c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2cgpA/struct-align/2cgpA.fssp-w0.5.mod', needed by `2cgpA/2cgpA-T0096-fssp-global.pw.a2m.gz'.
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 2cgpA
fixmode 2cgpA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 2cgpA/T0096-2cgpA-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -88.885742
Database has 2 sequences with 449 residues.
gzip -f 2cgpA/T0096-2cgpA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2cgpA/nostruct-align/2cgpA.t2k-w0.5.mod', needed by `2cgpA/2cgpA-T0096-local.pw.a2m.gz'.
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 2cgpA/T0096-2cgpA-vit.pw \
	 -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -86.012756
Database has 2 sequences with 449 residues.
gzip -f 2cgpA/T0096-2cgpA-vit.pw.a2m
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 2cgpA/T0096-2cgpA-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -170.206543
Database has 2 sequences with 449 residues.
gzip -f 2cgpA/T0096-2cgpA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2cgpA/xxxx-2cgpA-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1bi0 PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11251


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp.a2m.gz (16 sequences, 214 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/tmp.a2m.
Dropping 5 (of 16) duplicate sequences with differing IDs
Dropping 8 (of 16) sequences with > 80.0% id
3 sequences left after dropping 13 of 16 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/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-11251/tmp.a2m (3 sequences, 214 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11251 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 1bi0
fixmode 1bi0
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/1bi0-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/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:        -224.188019
Database has 2 sequences with 465 residues.
gzip -f 1bi0/1bi0-T0096-fssp-global.pw.a2m
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/T0096-1bi0-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -88.401550
Database has 2 sequences with 465 residues.
gzip -f 1bi0/T0096-1bi0-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bi0/nostruct-align/1bi0.t2k-w0.5.mod', needed by `1bi0/1bi0-T0096-local.pw.a2m.gz'.
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/T0096-1bi0-vit.pw \
	 -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -85.200073
Database has 2 sequences with 465 residues.
gzip -f 1bi0/T0096-1bi0-vit.pw.a2m
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/T0096-1bi0-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -177.937531
Database has 2 sequences with 465 residues.
gzip -f 1bi0/T0096-1bi0-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bi0/xxxx-1bi0-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1lea PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/1lea-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1l/1lea/struct-align/1lea.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11878/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:        -46.034336
Database has 3 sequences with 395 residues.
gzip -f 1lea/1lea-T0096-fssp-global.pw.a2m
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/T0096-1lea-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -68.321716
Database has 3 sequences with 395 residues.
gzip -f 1lea/T0096-1lea-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1l/1lea/nostruct-align/1lea.t2k-w0.5.mod', needed by `1lea/1lea-T0096-local.pw.a2m.gz'.
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/T0096-1lea-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -63.814381
Database has 3 sequences with 395 residues.
gzip -f 1lea/T0096-1lea-vit.pw.a2m
make 1lea
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1lea' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1lea/T0096-1lea-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1lea/info/1lea.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -116.042336
Database has 3 sequences with 395 residues.
gzip -f 1lea/T0096-1lea-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lea/xxxx-1lea-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1bia PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/1bia-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bia/struct-align/1bia.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23376/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:        -215.813034
Database has 3 sequences with 852 residues.
gzip -f 1bia/1bia-T0096-fssp-global.pw.a2m
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/T0096-1bia-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -68.247520
Database has 3 sequences with 852 residues.
gzip -f 1bia/T0096-1bia-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bia/nostruct-align/1bia.t2k-w0.5.mod', needed by `1bia/1bia-T0096-local.pw.a2m.gz'.
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/T0096-1bia-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -62.650837
Database has 3 sequences with 852 residues.
gzip -f 1bia/T0096-1bia-vit.pw.a2m
make 1bia
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bia' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bia/T0096-1bia-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bia/info/1bia.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -168.241745
Database has 3 sequences with 852 residues.
gzip -f 1bia/T0096-1bia-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bia/xxxx-1bia-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=2cgpA PRED2=2c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2cgpA/struct-align/2cgpA.fssp-w0.5.mod', needed by `2cgpA/2cgpA-T0096-fssp-global.pw.a2m.gz'.
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 2cgpA/T0096-2cgpA-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -65.374718
Database has 3 sequences with 649 residues.
gzip -f 2cgpA/T0096-2cgpA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2cgpA/nostruct-align/2cgpA.t2k-w0.5.mod', needed by `2cgpA/2cgpA-T0096-local.pw.a2m.gz'.
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 2cgpA/T0096-2cgpA-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -62.317059
Database has 3 sequences with 649 residues.
gzip -f 2cgpA/T0096-2cgpA-vit.pw.a2m
make 2cgpA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `2cgpA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 2cgpA/T0096-2cgpA-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cgpA/info/2cgpA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -137.477707
Database has 3 sequences with 649 residues.
gzip -f 2cgpA/T0096-2cgpA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2cgpA/xxxx-2cgpA-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1bi0 PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/1bi0-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bi0/struct-align/1bi0.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11251/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:        -277.274689
Database has 3 sequences with 679 residues.
gzip -f 1bi0/1bi0-T0096-fssp-global.pw.a2m
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/T0096-1bi0-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -64.761719
Database has 3 sequences with 679 residues.
gzip -f 1bi0/T0096-1bi0-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bi0/nostruct-align/1bi0.t2k-w0.5.mod', needed by `1bi0/1bi0-T0096-local.pw.a2m.gz'.
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/T0096-1bi0-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -61.235394
Database has 3 sequences with 679 residues.
gzip -f 1bi0/T0096-1bi0-vit.pw.a2m
make 1bi0
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1bi0' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1bi0/T0096-1bi0-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bi0/info/1bi0.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -149.639709
Database has 3 sequences with 679 residues.
gzip -f 1bi0/T0096-1bi0-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bi0/xxxx-1bi0-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)
make -k PRED=1b78A PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14464


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14464/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp.a2m.gz (4 sequences, 184 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14464/tmp.a2m.
Dropping 3 (of 4) duplicate sequences with differing IDs
1 sequences left after dropping 3 of 4 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14464/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14464/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-14464/tmp.a2m (1 sequences, 184 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14464/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14464 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
mkdir 1b78A
fixmode 1b78A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1b78A/1b78A-T0096-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1b78A/struct-align/1b78A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14464/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:        -270.032043
Database has 3 sequences with 616 residues.
gzip -f 1b78A/1b78A-T0096-fssp-global.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1b78A/T0096-1b78A-local.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -59.252338
Database has 3 sequences with 616 residues.
gzip -f 1b78A/T0096-1b78A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1b78A/nostruct-align/1b78A.t2k-w0.5.mod', needed by `1b78A/1b78A-T0096-local.pw.a2m.gz'.
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1b78A/T0096-1b78A-vit.pw \
	-i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -54.817017
Database has 3 sequences with 616 residues.
gzip -f 1b78A/T0096-1b78A-vit.pw.a2m
make 1b78A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t96'
make[2]: `1b78A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
hmmscore 1b78A/T0096-1b78A-global.pw -i T0096.t2k-w0.5.mod -db T0096.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b78A/info/1b78A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0096.t2k-w0.5.mod
T0096.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25261/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:        -128.487717
Database has 3 sequences with 616 residues.
gzip -f 1b78A/T0096-1b78A-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b78A/xxxx-1b78A-T0096-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t96'
make: [joints] Error 2 (ignored)