make -k T0087-181-end-blast.rdb T0087-181-end-double-blast.rdb
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87/t87-181-end'
make[1]: `T0087-181-end-blast.rdb' is up to date.
make[1]: `T0087-181-end-double-blast.rdb' is up to date.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87/t87-181-end'
make -k T0087-181-end.t2k.a2m.gz	\
	T0087-181-end.t2k.pa \
	T0087-181-end.t2k.pa.html \
	T0087-181-end.t2k.2d \
	T0087-181-end.t2k.tree \
	T0087-181-end.t2k_sorted.pa \
	T0087-181-end.t2k.tree.ps \
	T0087-181-end.t2k.tree-unroot.ps 
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t87/t87-181-end'
make[1]: `T0087-181-end.t2k.a2m.gz' is up to date.
make[1]: `T0087-181-end.t2k.pa' is up to date.
make[1]: `T0087-181-end.t2k.pa.html' is up to date.
make[1]: `T0087-181-end.t2k.2d' is up to date.
make[1]: `T0087-181-end.t2k.tree' is up to date.
make[1]: `T0087-181-end.t2k_sorted.pa' is up to date.
make[1]: `T0087-181-end.t2k.tree.ps' is up to date.
make[1]: `T0087-181-end.t2k.tree-unroot.ps' is up to date.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t87/t87-181-end'
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0087-181-end.t2k.2d.rdb T0087-181-end.t2k-2d.mod
/projects/compbio/bin/alpha.new/hmmscore T0087-181-end.t2k-2track \
	-trackmod T0087-181-end.t2k-w0.5.mod,T0087-181-end.t2k-2d.mod \
	-db /projects/compbio/experiments/models.97/indexes/t99.seqs,/projects/compbio/experiments/models.97/indexes/t99.2ds \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -dpstyle 0 \
	-select_score 4 -Emax 40.
SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39
T0087-181-end.t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6014/tmp.a2m
T0087-181-end.t2k-2d.mod(809):  Reading track 1 model from MODEL -- Model from 2nd structure file T0087-181-end.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
....
Average NLL-Simple NULL score:        -11.969192
Database has 3421 sequences with 771403 residues.