/projects/compbio/bin/alpha.new/hmmscore T0120.t2k-2track \ -trackmod T0120.t2k-w0.5.mod,T0120.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 T0120.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-23846/tmp.a2m T0120.t2k-2d.mod(2045): Reading track 1 model from MODEL -- Model from 2nd structure file T0120.t2k.2d.rdb Calculating Distances (. = 1000 sequences) .... Average NLL-Simple NULL score: -13.937958 Database has 3506 sequences with 788879 residues. /projects/compbio/bin/scripts/w0.5 T0120.remote-t2k.a2m.gz T0120.remote-t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10954 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp -alignfile T0120.remote-t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file T0120.remote-t2k.a2m.gz (28 sequences, 336 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m. Dropping 7 (of 28) duplicate sequences with differing IDs Dropping 7 (of 28) duplicate sequences with identical IDs Dropping 12 (of 28) sequences with > 80.0% id 8 sequences left after dropping 20 of 28 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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 v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m (8 sequences, 336 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.mod T0120.remote-t2k-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10954