/projects/compbio/experiments/models.97/scripts2k/target2k -out T0120-211-end.remote-t2k \ -seed T0120-211-end.t2k.a2m.gz -all \ -iter 3 \ -thresholds 0.1,1,10 \ -prefilter_thresholds 1000,1000,2000 @@@@ chgrp protein /projects/compbio/tmp/target2k-beta-15644 @@@@ gunzip -c /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.t2k.a2m.gz > m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:52 # About to count sequences in /projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are prefilter: 1000, actual: 0.1 prefilter: 1000, actual: 1 prefilter: 2000, actual: 10 /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.6 /projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 553635 reverse_diff= 4 /projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 20000 /projects/compbio/experiments/models.97/scripts2k/target2k: db=/projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_method=1 aweight_exponent=10 /projects/compbio/experiments/models.97/scripts2k/target2k: force_seed=1 constraints=1 /projects/compbio/experiments/models.97/scripts2k/target2k: jump_in=0.2 jump_out=1 fimstrength=1 fimtrans=-1 @@@@ blast-prefilter -out prefilter -seed m0.a2m -prefilter_thresholds 1000,1000,2000 -db /projects/compbio/data/nrp/nr -blast_max_report 20000 @@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-beta-14609 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /export/projects/compbio/tmp/target2k-beta-15644/prefilter_1.fa, 1000 For /export/projects/compbio/tmp/target2k-beta-15644/prefilter_2.fa, 1000 For /export/projects/compbio/tmp/target2k-beta-15644/prefilter_3.fa, 2000 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr @@@@ uniqueseq init -alignfile /export/projects/compbio/tmp/target2k-beta-15644/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /export/projects/compbio/tmp/target2k-beta-15644/m0.a2m (3 sequences, 126 columns) as A2M alignment. Writing sequence output to init.a2m. Dropping 1 (of 3) duplicate sequences with differing IDs 2 sequences left after dropping 1 of 3 sequences. @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta E=2000 V=20000 B=0 -gi > 1.fasta-blast.out Searched 553635 sequences # parsing wu-blastp output @@@@ rm -f 1.fasta < /dev/null @@@@ rm -f 1.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 2.fasta E=2000 V=20000 B=0 -gi > 2.fasta-blast.out Searched 553635 sequences # parsing wu-blastp output @@@@ rm -f 2.fasta < /dev/null @@@@ rm -f 2.fasta-blast.out < /dev/null # Extracting hits in FASTA format from /projects/compbio/data/nrp/nr @@@@ rm -rf /projects/compbio/tmp/blast-prefilter-beta-14609 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file m0.a2m (3 sequences, 126 columns) as A2M alignment. # About to count sequences in m0.a2m # About to count sequences in prefilter_1.fa @@@@ modelfromalign tmp_1-a -alignfile m0.a2m \ -insert /projects/compbio/lib/gap1.5.regularizer \ -aweight_bits 0.8\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints m0.cst -constraints_out tmp_1-a.cst Reading parameter file /projects/compbio/lib/gap1.5.regularizer /projects/compbio/lib/gap1.5.regularizer(1): Reading REGULARIZER: gap1.5. Weak regularizer, gaps average 1.5, matches average 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file m0.a2m (3 sequences, 126 columns) as A2M alignment. @@@@ hmmscore tmp_1-a -i tmp_1-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -simple_threshold -19.5268458162001 -Emax 0.1 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.1\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.158730158730159 -db prefilter_1.fa -constraints tmp_1-a.cst -constraints_out tmp_1-a-md.cst Reading parameter file tmp_1-a.mod tmp_1-a.mod(21): Reading MODEL -- Model from alignment file m0.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) ...... Average NLL-Simple NULL score: -8.896151 Database has 5841 sequences with 3202397 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_1-a.mult (2 sequences, 126 columns) as A2M alignment. Reading scores from file tmp_1-a.mstat Writing sequence output to tmp_1-a-sort.a2m. @@@@ cat m0.a2m tmp_1-a-sort.a2m > tmp_1-a.train.seq @@@@ cat m0.cst tmp_1-a-md.cst > tmp_1-a.train.cst # About to count sequences in tmp_1-a.train.seq # num_seqs=5 nll_thresh=-15.5268458162001 frac_id=0.999999999999974 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.999999999999974 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_1-a.train.seq (5 sequences, 126 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 2 (of 5) duplicate sequences with differing IDs Dropping 2 (of 5) duplicate sequences with identical IDs 2 sequences left after dropping 3 of 5 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_1-a.train.seq \ -aweight_bits 0.8\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_1-a.train.seq (2 sequences, 126 columns) as A2M alignment. @@@@ buildmodel tmp_1-b -insert tmp_1-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_1-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/gap1.5.regularizer -sequence_weights tmp_1-a.w -constraints tmp_1-a.train.cst Reading parameter file tmp_1-a.mod tmp_1-a.mod(21): Reading MODEL -- Model from alignment file m0.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/gap1.5.regularizer /projects/compbio/lib/gap1.5.regularizer(1): Reading REGULARIZER: gap1.5. Weak regularizer, gaps average 1.5, matches average 10 SAM: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 Warning: only 2 training sequences; Buildmodel needs 5--100 sequences for best results unless -sequence_models is used. -345.39 -337.70 -341.55 5.44 3 0 127 @@@@ hmmscore tmp_1-b -i tmp_1-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -19.5268458162001 -Emax 0.1 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.158730158730159 \ -align_short 5 -mdEmax 0.1 -constraints tmp_1-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.cst Reading parameter file tmp_1-b.mod tmp_1-b.mod(18): Reading MODEL -- Final model for run tmp_1-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -111.551949 Database has 15 sequences with 6503 residues. @@@@ cp -f tmp_1-b.mult /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.a2m \ -insert /projects/compbio/lib/stiff-gap5.regularizer \ -aweight_bits 0.7\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.cst -constraints_out tmp_2-a.cst Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.a2m (5 sequences, 126 columns) as A2M alignment. @@@@ hmmscore tmp_2-a -i tmp_2-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -simple_threshold -17.2242590975847 -Emax 1 \ -adpstyle 1 \ -align_short 0 -mdEmax 1\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.158730158730159 -db prefilter_2.fa -constraints tmp_2-a.cst -constraints_out tmp_2-a-md.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) ...... Average NLL-Simple NULL score: -12.739586 Database has 5841 sequences with 3202397 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_2-a.mult (4 sequences, 126 columns) as A2M alignment. Reading scores from file tmp_2-a.mstat Writing sequence output to tmp_2-a-sort.a2m. @@@@ cat m0.a2m tmp_2-a-sort.a2m > tmp_2-a.train.seq @@@@ cat m0.cst tmp_2-a-md.cst > tmp_2-a.train.cst # About to count sequences in tmp_2-a.train.seq # num_seqs=7 nll_thresh=-13.2242590975847 frac_id=0.999999995005569 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.999999995005569 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_2-a.train.seq (7 sequences, 126 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 7) duplicate sequences with differing IDs Dropping 3 (of 7) duplicate sequences with identical IDs 3 sequences left after dropping 4 of 7 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_2-a.train.seq \ -aweight_bits 0.7\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_2-a.train.seq (3 sequences, 126 columns) as A2M alignment. @@@@ buildmodel tmp_2-b -insert tmp_2-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_2-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/stiff-gap5.regularizer -sequence_weights tmp_2-a.w -constraints tmp_2-a.train.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_1.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 Warning: only 3 training sequences; Buildmodel needs 5--100 sequences for best results unless -sequence_models is used. -344.63 -105.29 -261.60 135.46 10 0 127 @@@@ hmmscore tmp_2-b -i tmp_2-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -17.2242590975847 -Emax 1 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.158730158730159 \ -align_short 5 -mdEmax 1 -constraints tmp_2-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.cst Reading parameter file tmp_2-b.mod tmp_2-b.mod(18): Reading MODEL -- Final model for run tmp_2-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) .. Average NLL-Simple NULL score: -11.667490 Database has 1247 sequences with 712390 residues. @@@@ cp -f tmp_2-b.mult /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.6\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.cst -constraints_out tmp_3-a.cst 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 /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.a2m (10 sequences, 126 columns) as A2M alignment. @@@@ hmmscore tmp_3-a -i tmp_3-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -simple_threshold -14.9216577482315 -Emax 10 \ -adpstyle 1 \ -align_short 0 -mdEmax 10\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.158730158730159 -db prefilter_3.fa -constraints tmp_3-a.cst -constraints_out tmp_3-a-md.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) ...... Average NLL-Simple NULL score: -7.794395 Database has 5841 sequences with 3202397 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_3-a.mult (8 sequences, 126 columns) as A2M alignment. Reading scores from file tmp_3-a.mstat Writing sequence output to tmp_3-a-sort.a2m. @@@@ cat m0.a2m tmp_3-a-sort.a2m > tmp_3-a.train.seq @@@@ cat m0.cst tmp_3-a-md.cst > tmp_3-a.train.cst # About to count sequences in tmp_3-a.train.seq # num_seqs=11 nll_thresh=-10.9216577482315 frac_id=0.999961000903255 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.999961000903255 -a2mdots 0 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp_3-a.train.seq (11 sequences, 126 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 11) duplicate sequences with differing IDs Dropping 3 (of 11) duplicate sequences with identical IDs 7 sequences left after dropping 4 of 11 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_3-a.train.seq \ -aweight_bits 0.6\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file tmp_3-a.train.seq (7 sequences, 126 columns) as A2M alignment. @@@@ buildmodel tmp_3-b -insert tmp_3-a.mod\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_3-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/fssp-trained.regularizer -sequence_weights tmp_3-a.w -constraints tmp_3-a.train.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_2.a2m Command line option(48): internal_weight has already been set. Using 0. 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: buildmodel v3.2 (July 31, 2000) compiled 07/31/00_14:08:12 -345.25 -30.40 -137.50 143.26 16 0 127 @@@@ hmmscore tmp_3-b -i tmp_3-b.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -14.9216577482315 -Emax 10 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.158730158730159 \ -align_short 5 -mdEmax 10 -constraints tmp_3-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_3.cst Reading parameter file tmp_3-b.mod tmp_3-b.mod(18): Reading MODEL -- Final model for run tmp_3-b SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -20.060200 Database has 186 sequences with 70842 residues. @@@@ cp -f tmp_3-b.mult /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_3.a2m @@@@ modelfromalign tmp_4-a -alignfile /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_3.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.6\ -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \ -aweight_method 1\ -aweight_exponent 10 -constraints /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_3.cst -constraints_out tmp_4-a.cst 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 /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_3.a2m (12 sequences, 126 columns) as A2M alignment. @@@@ hmmscore tmp_4-a -i tmp_4-a.mod -fimtrans -1\ -fimstrength 1\ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -binary_output 1\ -prior_library /projects/compbio/lib/recode3.20comp \ -a2mdots 0 \ -a protein \ -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\ -dpstyle 0 \ -subtract_null 4 -sort 2 \ -db_size 553635 \ -simple_threshold -14.9216577482315 -Emax 10 \ -adpstyle 5 \ -align_short 0 -mdEmax 10\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.158730158730159 -db prefilter_3.fa -constraints tmp_4-a.cst -constraints_out tmp_4-a-md.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(21): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k_3.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) ...... Average NLL-Simple NULL score: -7.726974 Database has 5841 sequences with 3202397 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:48 Reading alignment file tmp_4-a.mult (8 sequences, 126 columns) as A2M alignment. Reading scores from file tmp_4-a.mstat Writing sequence output to tmp_4-a-sort.a2m. @@@@ cat m0.a2m tmp_4-a-sort.a2m > tmp_4-a.train.seq @@@@ cat m0.cst tmp_4-a-md.cst > tmp_4-a.train.cst @@@@ cp tmp_4-a.train.seq /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k.a2m @@@@ cp tmp_4-a.train.cst /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-beta-15644 < /dev/null gzip -9f T0120-211-end.remote-t2k.a2m gunzip -c T0120-211-end.remote-t2k.a2m.gz > tmp.a2m a2m2html -a2m_in tmp.a2m -retrieve > T0120-211-end.remote-t2k.pa.html SAM: /projects/compbio/bin/alpha/prettyalign v3.2 (July 31, 2000) compiled 08/11/00_16:27:51 rm tmp.a2m /projects/compbio/experiments/models.97/scripts99/score-target -alignment T0120-211-end.remote-t2k.a2m.gz -build w0.5 \ -db /projects/compbio/data/pdb/all-protein \ -Emax 40.0 \ -viterbi 0 -sw_score 2 \ -output T0120-211-end.remote-t2k-w0.5-pdb.rdb PATH=.:/projects/compbio/experiments/models.97/scripts99:/projects/compbio/bin:/projects/compbio/bin/alpha:/projects/compbio/bin/hmmscripts:/projects/compbio/bin/scripts:/sbin:/usr/sbin:/bin:/usr/bin:/usr/local/gnu/bin:/usr/local/share/request/bin:/usr/local/bin @@@@ mkdir /projects/compbio/tmp/score-target-8738 @@@@ mkdir /projects/compbio/tmp/score-target-8738/for-scorescript @@@@ /projects/compbio/experiments/models.97/scripts99/score-mods-vs-seqs.pl -root_tmp /projects/compbio/tmp/score-target-8738/for-scorescript -a2msfile /projects/compbio/tmp/score-target-8738/score-target.a2m \ -buildscript /projects/compbio/bin/scripts/w0.5 -seqfile /projects/compbio/data/pdb/all-protein -Emax 40.0 -viterbi 0 \ -sw_score 2 -output /projects/compbio/tmp/score-target-8738/score-target.op @@@@ chgrp protein /projects/compbio/tmp/score-target-8738/for-scorescript/split-tmp @@@@ chgrp protein /projects/compbio/tmp/score-target-8738/for-scorescript/split-tmp @@@@ /projects/compbio/bin/scripts/w0.5 /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k.a2m.gz /projects/compbio/tmp/score-target-8738/for-scorescript/split-tmp/beta-19719/T0120-211-end.remote-t2k.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12390 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12390/tmp -alignfile /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.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 /export/projects/compbio/experiments/casp4/t120/t120-211-end/T0120-211-end.remote-t2k.a2m.gz (11 sequences, 126 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12390/tmp.a2m. Dropping 3 (of 11) duplicate sequences with differing IDs Dropping 3 (of 11) duplicate sequences with identical IDs Dropping 1 (of 11) sequences with > 80.0% id 6 sequences left after dropping 5 of 11 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12390/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12390/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-12390/tmp.a2m (6 sequences, 126 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12390/tmp.mod /projects/compbio/tmp/score-target-8738/for-scorescript/split-tmp/beta-19719/T0120-211-end.remote-t2k.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12390