make -k T0098-blast.rdb T0098-double-blast.rdb make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t98' /projects/compbio/experiments/casp4/scripts/single-blast -q T0098.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > T0098-blast.rdb starting T0098 with E=10 /projects/compbio/experiments/casp4/scripts/double-blast -q T0098.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > T0098-double-blast.rdb starting T0098 with E=0.000050 T0098 T0098 blasting: T0098 gi|134739|sp|P06534|SP0A_BACSU_149:267 blasting: T0098 gi|1711470|sp|P52928|SP0A_BACAN_144:214 blasting: T0098 gi|1711471|sp|P52929|SP0A_BACBR_146:212 blasting: T0098 gi|1711472|sp|P52930|SP0A_BACCE_80:150 blasting: T0098 gi|1711473|sp|P52931|SP0A_BACCI_142:210 blasting: T0098 gi|1711474|sp|P52932|SP0A_BACME_142:212 blasting: T0098 gi|1711475|sp|P52933|SP0A_BACPU_86:191 blasting: T0098 gi|1174405|sp|P42012|SP0A_BACSH_149:263 blasting: T0098 gi|1711476|sp|P52934|SP0A_BACST_76:146 blasting: T0098 gi|497963|gb|AAA18879.1|_97:166 blasting: T0098 gi|1711498|sp|P52936|SP0A_CLOAB_156:223 blasting: T0098 gi|1711478|sp|P52937|SP0A_CLOBU_94:161 blasting: T0098 gi|1711480|sp|P52939|SP0A_CLOIN_153:265 blasting: T0098 gi|1711481|sp|P52940|SP0A_CLOPA_155:267 blasting: T0098 gi|1711482|sp|P52941|SP0A_MOOTH_140:206 blasting: T0098 gi|1711477|sp|P52935|SP0A_BACTU_144:264 blasting: T0098 gi|1020324|gb|AAA79509.1|_89:154 blasting: T0098 gi|1130609|emb|CAA63989.1|_158:256 blasting: T0098 gi|1711479|sp|P52938|SP0A_CLODI_158:270 blasting: T0098 gi|2119850|pir||S60873_89:192 blasting: T0098 gi|2119851|pir||S60870_80:151 blasting: T0098 gi|2119852|pir||S60875_76:147 blasting: T0098 gi|2119853|pir||S60878_97:162 blasting: T0098 gi|2119854|pir||S60876_97:167 blasting: T0098 gi|2119855|pir||S60874_145:264 blasting: T0098 gi|2119856|pir||S60880_156:268 blasting: T0098 gi|2119857|pir||S60868_144:215 blasting: T0098 gi|2119858|pir||S60871_145:211 blasting: T0098 gi|2119859|pir||S60872_142:213 blasting: T0098 gi|2119861|pir||S60877_150:224 blasting: T0098 gi|2119862|pir||S60881_141:207 blasting: T0098 gi|2144249|pir||S60879_154:266 blasting: T0098 gi|2654216|emb|CAA05307.1|_139:259 blasting: T0098 gi|7576238|emb|CAB87985.1|_156:273 blasting: T0098 gi|7576241|emb|CAB87987.1|_172:292 blasting: make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98' make -k T0098.t2k.a2m.gz \ T0098.t2k.pa \ T0098.t2k.pa.html \ T0098.t2k.2d \ T0098.t2k.tree \ T0098.t2k_sorted.pa \ T0098.t2k.tree.ps \ T0098.t2k.tree-unroot.ps make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t98' /projects/compbio/experiments/models.97/scripts2k/target2k -out T0098.t2k \ -seed T0098.seq \ -all @@@@ chgrp protein /projects/compbio/tmp/target2k-eclipse-24730 @@@@ cp /projects/compbio/experiments/casp4/t98/T0098.seq m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:44 # About to count sequences in /projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are prefilter: 0.01, actual: 0.0001 prefilter: 1, actual: 0.0002 prefilter: 10, actual: 0.001 prefilter: 400, actual: 0.005 /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.6, 0.5 /projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 509169 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 0.01,1,10,400 -db /projects/compbio/data/nrp/nr -blast_max_report 20000 @@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-eclipse-31723 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /projects/compbio/tmp/target2k-eclipse-24730/prefilter_1.fa, 0.01 For /projects/compbio/tmp/target2k-eclipse-24730/prefilter_2.fa, 1 For /projects/compbio/tmp/target2k-eclipse-24730/prefilter_3.fa, 10 For /projects/compbio/tmp/target2k-eclipse-24730/prefilter_4.fa, 400 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr @@@@ uniqueseq init -alignfile /projects/compbio/tmp/target2k-eclipse-24730/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /projects/compbio/tmp/target2k-eclipse-24730/m0.a2m (1 sequences, 121 columns) as A2M alignment. Writing sequence output to init.a2m. No sequences have been droppd. @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta E=400 V=20000 B=0 -gi > 1.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 1.fasta < /dev/null @@@@ rm -f 1.fasta-blast.out < /dev/null # Extracting hits in FASTA format from /projects/compbio/data/nrp/nr @@@@ rm -rf /projects/compbio/tmp/blast-prefilter-eclipse-31723 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (1 sequences, 121 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (1 sequences, 121 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 509169 \ -simple_threshold -26.3508756357805 -Emax 0.0001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file m0.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -118.728569 Database has 35 sequences with 7648 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_1-a.mult (35 sequences, 121 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=36 nll_thresh=-22.3508756357805 frac_id=0.998393552717008 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.998393552717008 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_1-a.train.seq (36 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 36) duplicate sequences with differing IDs Dropping 11 (of 36) sequences with > 99.8% id 22 sequences left after dropping 14 of 36 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_1-a.train.seq (22 sequences, 121 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(23): 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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -338.16 -68.34 -133.54 69.35 6 0 122 @@@@ 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 509169 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -26.3508756357805 -Emax 0.0001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 0.0001 -constraints tmp_1-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.t2k_1.cst Reading parameter file tmp_1-b.mod tmp_1-b.mod(20): Reading MODEL -- Final model for run tmp_1-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -148.578384 Database has 36 sequences with 7769 residues. @@@@ cp -f tmp_1-b.mult /projects/compbio/experiments/casp4/t98/T0098.t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.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 /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_1.a2m (36 sequences, 121 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 509169 \ -simple_threshold -25.6577284550241 -Emax 0.0002 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0002\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_1.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -126.061989 Database has 38 sequences with 8247 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_2-a.mult (35 sequences, 121 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=36 nll_thresh=-21.6577284550241 frac_id=0.998053292088553 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.998053292088553 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_2-a.train.seq (36 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 36) duplicate sequences with differing IDs Dropping 5 (of 36) sequences with > 99.8% id 28 sequences left after dropping 8 of 36 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_2-a.train.seq (28 sequences, 121 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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -336.61 -88.02 -138.66 54.13 4 0 122 @@@@ 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 509169 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -25.6577284550241 -Emax 0.0002 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 0.0002 -constraints tmp_2-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.t2k_2.cst Reading parameter file tmp_2-b.mod tmp_2-b.mod(20): Reading MODEL -- Final model for run tmp_2-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -141.931854 Database has 36 sequences with 7769 residues. @@@@ cp -f tmp_2-b.mult /projects/compbio/experiments/casp4/t98/T0098.t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.t2k_2.a2m \ -insert /projects/compbio/lib/stiff-gap5.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 /projects/compbio/experiments/casp4/t98/T0098.t2k_2.cst -constraints_out tmp_3-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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_2.a2m (36 sequences, 121 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 509169 \ -simple_threshold -24.0482905410188 -Emax 0.001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_2.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -93.197754 Database has 51 sequences with 9472 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_3-a.mult (35 sequences, 121 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=36 nll_thresh=-20.0482905410188 frac_id=0.99696006850521 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.99696006850521 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_3-a.train.seq (36 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 36) duplicate sequences with differing IDs Dropping 5 (of 36) sequences with > 99.7% id 28 sequences left after dropping 8 of 36 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_3-a.train.seq (28 sequences, 121 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/stiff-gap5.regularizer -sequence_weights tmp_3-a.w -constraints tmp_3-a.train.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_2.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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -336.62 -82.74 -132.05 53.98 4 0 122 @@@@ 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 509169 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -24.0482905410188 -Emax 0.001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 0.001 -constraints tmp_3-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.t2k_3.cst Reading parameter file tmp_3-b.mod tmp_3-b.mod(20): Reading MODEL -- Final model for run tmp_3-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -135.536133 Database has 36 sequences with 7769 residues. @@@@ cp -f tmp_3-b.mult /projects/compbio/experiments/casp4/t98/T0098.t2k_3.a2m # About to count sequences in prefilter_4.fa @@@@ modelfromalign tmp_4-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.t2k_3.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.5\ -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 /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_3.a2m (36 sequences, 121 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 509169 \ -simple_threshold -22.4388526207288 -Emax 0.005 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -db prefilter_4.fa -constraints tmp_4-a.cst -constraints_out tmp_4-a-md.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_3.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -18.763956 Database has 464 sequences with 83105 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_4-a.mult (35 sequences, 121 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 # About to count sequences in tmp_4-a.train.seq # num_seqs=36 nll_thresh=-18.4388526207288 frac_id=0.995256566304689 @@@@ uniqueseq thinned_tmp -alignfile tmp_4-a.train.seq -a protein \ -percent_id 0.995256566304689 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_4-a.train.seq (36 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 36) duplicate sequences with differing IDs Dropping 5 (of 36) sequences with > 99.5% id 28 sequences left after dropping 8 of 36 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_4-a.train.seq \ -aweight_bits 0.5\ -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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_4-a.train.seq (28 sequences, 121 columns) as A2M alignment. @@@@ buildmodel tmp_4-b -insert 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\ -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_4-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/fssp-trained.regularizer -sequence_weights tmp_4-a.w -constraints tmp_4-a.train.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_3.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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -336.91 -82.28 -128.49 52.42 5 0 122 @@@@ hmmscore tmp_4-b -i tmp_4-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 509169 \ -db m0.a2m -db tmp_4-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -22.4388526207288 -Emax 0.005 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 0.005 -constraints tmp_4-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.t2k_4.cst Reading parameter file tmp_4-b.mod tmp_4-b.mod(20): Reading MODEL -- Final model for run tmp_4-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -129.576996 Database has 36 sequences with 7769 residues. @@@@ cp -f tmp_4-b.mult /projects/compbio/experiments/casp4/t98/T0098.t2k_4.a2m @@@@ modelfromalign tmp_5-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.t2k_4.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.5\ -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 /projects/compbio/experiments/casp4/t98/T0098.t2k_4.cst -constraints_out tmp_5-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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_4.a2m (36 sequences, 121 columns) as A2M alignment. @@@@ hmmscore tmp_5-a -i tmp_5-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 509169 \ -simple_threshold -22.4388526207288 -Emax 0.005 \ -adpstyle 5 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -db prefilter_4.fa -constraints tmp_5-a.cst -constraints_out tmp_5-a-md.cst Reading parameter file tmp_5-a.mod tmp_5-a.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.t2k_4.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -18.763956 Database has 464 sequences with 83105 residues. @@@@ sortseq tmp_5-a-sort -alignfile tmp_5-a.mult \ -NLLfile tmp_5-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_5-a.mult (35 sequences, 121 columns) as A2M alignment. Reading scores from file tmp_5-a.mstat Writing sequence output to tmp_5-a-sort.a2m. @@@@ cat m0.a2m tmp_5-a-sort.a2m > tmp_5-a.train.seq @@@@ cat m0.cst tmp_5-a-md.cst > tmp_5-a.train.cst @@@@ cp tmp_5-a.train.seq /projects/compbio/experiments/casp4/t98/T0098.t2k.a2m @@@@ cp tmp_5-a.train.cst /projects/compbio/experiments/casp4/t98/T0098.t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-eclipse-24730 < /dev/null gzip -f T0098.t2k.a2m T0098.t2k_*.a2m prettyalign T0098.t2k.a2m.gz -m8 -i -n -L3333 > T0098.t2k.pa SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 gunzip -c T0098.t2k.a2m.gz > tmp.a2m a2m2html -a2m_in tmp.a2m -retrieve > T0098.t2k.pa.html SAM: /projects/compbio/bin/alpha/prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 rm tmp.a2m echo ReadNeuralNet /projects/compbio/usr/karplus/predict-2nd/testing/networks/overrep-2500-IDaa13-5-9-7-10-5-10-11-ehl2-seeded4-stride-trained.net > tmp.script echo ReadA2M T0098.t2k.a2m.gz >> tmp.script echo PrintPrediction T0098.t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0098.t2k.2d.seq >> tmp.script echo PrintRDB T0098.t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-9-7-10-5-10-11-ehl2-seeded4-stride-trained.net # command:# Reading A2M format from T0098.t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0098.t2k.a2m with 36 sequences, total weight= 3.50994 avg weight= 0.0974983 11 iterations Regularizing alignment for T0098.t2k.a2m.gz # After reading T0098.t2k.a2m.gz, have 121 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0098.t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0098.t2k.2d.seq # command:# Network initialization done # Printing prediction to T0098.t2k.2d.rdb # command:rm tmp.script gunzip -f T0098.t2k.a2m.gz /projects/compbio/usr/karplus/src/phytree/phytree -o -i -r flat T0098.t2k T0098.t2k.a2m /projects/compbio/lib/recode2.20comp Prior library /projects/compbio/lib/recode2.20comp read. Reading alignment file T0098.t2k.a2m (36 sequences) as A2M alignment. Alignment T0098.t2k.a2m read. Adding sequences:0 10 20 30 One dot for every 10 merges: .... Merges done. CPU = user 0: 0: 7 system 0: 0: 0 gzip -f T0098.t2k.a2m gzip -f T0098.t2k_sorted.a2m rm T0098.t2k.phytrace T0098.t2k.tree_weight prettyalign T0098.t2k_sorted.a2m.gz -m8 -i -n -L3333 > T0098.t2k_sorted.pa SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 /projects/compbio/usr/karplus/src/phytree/dg T0098.t2k.tree /projects/compbio/usr/karplus/src/phytree/dtree T0098.t2k.tree make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t98' /projects/compbio/experiments/models.97/scripts99/score-target -alignment T0098.t2k.a2m.gz -build w0.5 \ -db /projects/compbio/data/pdb/all-protein \ -Emax 40.0 \ -viterbi 0 -sw_score 2 \ -output T0098.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-1198 @@@@ mkdir /projects/compbio/tmp/score-target-1198/for-scorescript @@@@ /projects/compbio/experiments/models.97/scripts99/score-mods-vs-seqs.pl -root_tmp /projects/compbio/tmp/score-target-1198/for-scorescript -a2msfile /projects/compbio/tmp/score-target-1198/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-1198/score-target.op @@@@ chgrp protein /projects/compbio/tmp/score-target-1198/for-scorescript/split-tmp @@@@ chgrp protein /projects/compbio/tmp/score-target-1198/for-scorescript/split-tmp @@@@ /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/casp4/t98/T0098.t2k.a2m.gz /projects/compbio/tmp/score-target-1198/for-scorescript/split-tmp/eclipse-23738/T0098.t2k.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016/tmp -alignfile /projects/compbio/experiments/casp4/t98/T0098.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/casp4/t98/T0098.t2k.a2m.gz (36 sequences, 121 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016/tmp.a2m. Dropping 2 (of 36) duplicate sequences with differing IDs Dropping 27 (of 36) sequences with > 80.0% id 7 sequences left after dropping 29 of 36 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016/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-eclipse-30016/tmp.a2m (7 sequences, 121 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016/tmp.mod /projects/compbio/tmp/score-target-1198/for-scorescript/split-tmp/eclipse-23738/T0098.t2k.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-30016 m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:44 # 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= 509169 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-eclipse-6842 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /projects/compbio/tmp/target2k-eclipse-7985/prefilter_1.fa, 1000 For /projects/compbio/tmp/target2k-eclipse-7985/prefilter_2.fa, 1000 For /projects/compbio/tmp/target2k-eclipse-7985/prefilter_3.fa, 2000 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr @@@@ uniqueseq init -alignfile /projects/compbio/tmp/target2k-eclipse-7985/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /projects/compbio/tmp/target2k-eclipse-7985/m0.a2m (36 sequences, 121 columns) as A2M alignment. Writing sequence output to init.a2m. Dropping 2 (of 36) duplicate sequences with differing IDs Dropping 5 (of 36) sequences with > 100.0% id 29 sequences left after dropping 7 of 36 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 509169 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 509169 sequences # parsing wu-blastp output @@@@ rm -f 2.fasta < /dev/null @@@@ rm -f 2.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 3.fasta E=2000 V=20000 B=0 -gi > 3.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 3.fasta < /dev/null @@@@ rm -f 3.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 4.fasta E=2000 V=20000 B=0 -gi > 4.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 4.fasta < /dev/null @@@@ rm -f 4.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 5.fasta E=2000 V=20000 B=0 -gi > 5.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 5.fasta < /dev/null @@@@ rm -f 5.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 6.fasta E=2000 V=20000 B=0 -gi > 6.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 6.fasta < /dev/null @@@@ rm -f 6.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 7.fasta E=2000 V=20000 B=0 -gi > 7.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 7.fasta < /dev/null @@@@ rm -f 7.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 8.fasta E=2000 V=20000 B=0 -gi > 8.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 8.fasta < /dev/null @@@@ rm -f 8.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 9.fasta E=2000 V=20000 B=0 -gi > 9.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 9.fasta < /dev/null @@@@ rm -f 9.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 10.fasta E=2000 V=20000 B=0 -gi > 10.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 10.fasta < /dev/null @@@@ rm -f 10.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 11.fasta E=2000 V=20000 B=0 -gi > 11.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 11.fasta < /dev/null @@@@ rm -f 11.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 12.fasta E=2000 V=20000 B=0 -gi > 12.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 12.fasta < /dev/null @@@@ rm -f 12.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 13.fasta E=2000 V=20000 B=0 -gi > 13.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 13.fasta < /dev/null @@@@ rm -f 13.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 14.fasta E=2000 V=20000 B=0 -gi > 14.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 14.fasta < /dev/null @@@@ rm -f 14.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 15.fasta E=2000 V=20000 B=0 -gi > 15.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 15.fasta < /dev/null @@@@ rm -f 15.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 16.fasta E=2000 V=20000 B=0 -gi > 16.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 16.fasta < /dev/null @@@@ rm -f 16.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 17.fasta E=2000 V=20000 B=0 -gi > 17.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 17.fasta < /dev/null @@@@ rm -f 17.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 18.fasta E=2000 V=20000 B=0 -gi > 18.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 18.fasta < /dev/null @@@@ rm -f 18.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 19.fasta E=2000 V=20000 B=0 -gi > 19.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 19.fasta < /dev/null @@@@ rm -f 19.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 20.fasta E=2000 V=20000 B=0 -gi > 20.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 20.fasta < /dev/null @@@@ rm -f 20.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 21.fasta E=2000 V=20000 B=0 -gi > 21.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 21.fasta < /dev/null @@@@ rm -f 21.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 22.fasta E=2000 V=20000 B=0 -gi > 22.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 22.fasta < /dev/null @@@@ rm -f 22.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 23.fasta E=2000 V=20000 B=0 -gi > 23.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 23.fasta < /dev/null @@@@ rm -f 23.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 24.fasta E=2000 V=20000 B=0 -gi > 24.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 24.fasta < /dev/null @@@@ rm -f 24.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 25.fasta E=2000 V=20000 B=0 -gi > 25.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 25.fasta < /dev/null @@@@ rm -f 25.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 26.fasta E=2000 V=20000 B=0 -gi > 26.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 26.fasta < /dev/null @@@@ rm -f 26.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 27.fasta E=2000 V=20000 B=0 -gi > 27.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 27.fasta < /dev/null @@@@ rm -f 27.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 28.fasta E=2000 V=20000 B=0 -gi > 28.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 28.fasta < /dev/null @@@@ rm -f 28.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 29.fasta E=2000 V=20000 B=0 -gi > 29.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 29.fasta < /dev/null @@@@ rm -f 29.fasta-blast.out < /dev/null # Extracting hits in FASTA format from /projects/compbio/data/nrp/nr @@@@ rm -rf /projects/compbio/tmp/blast-prefilter-eclipse-6842 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (36 sequences, 121 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (36 sequences, 121 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 509169 \ -simple_threshold -19.4431201605963 -Emax 0.1 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.1\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file m0.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) .................. Average NLL-Simple NULL score: -8.792619 Database has 17012 sequences with 5858216 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_1-a.mult (35 sequences, 121 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=71 nll_thresh=-15.4431201605962 frac_id=0.918391945907812 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.918391945907812 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_1-a.train.seq (71 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 5 (of 71) duplicate sequences with differing IDs Dropping 5 (of 71) duplicate sequences with identical IDs Dropping 48 (of 71) sequences with > 91.8% id 13 sequences left after dropping 58 of 71 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_1-a.train.seq (13 sequences, 121 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(23): 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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -337.95 -67.09 -167.05 92.80 5 0 122 @@@@ 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 509169 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -19.4431201605963 -Emax 0.1 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 0.1 -constraints tmp_1-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_1.cst Reading parameter file tmp_1-b.mod tmp_1-b.mod(20): Reading MODEL -- Final model for run tmp_1-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -202.562515 Database has 71 sequences with 10911 residues. @@@@ cp -f tmp_1-b.mult /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.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 /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_1.a2m (71 sequences, 121 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 509169 \ -simple_threshold -17.1405333000143 -Emax 1 \ -adpstyle 1 \ -align_short 0 -mdEmax 1\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_1.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) .................. Average NLL-Simple NULL score: -11.892231 Database has 17012 sequences with 5858216 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_2-a.mult (35 sequences, 121 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=71 nll_thresh=-13.1405333000143 frac_id=0.891374864189948 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.891374864189948 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_2-a.train.seq (71 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 5 (of 71) duplicate sequences with differing IDs Dropping 5 (of 71) duplicate sequences with identical IDs Dropping 54 (of 71) sequences with > 89.1% id 10 sequences left after dropping 61 of 71 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_2-a.train.seq (10 sequences, 121 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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -336.68 -89.45 -167.54 71.24 5 0 122 @@@@ 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 509169 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -17.1405333000143 -Emax 1 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 1 -constraints tmp_2-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_2.cst Reading parameter file tmp_2-b.mod tmp_2-b.mod(20): Reading MODEL -- Final model for run tmp_2-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -192.451920 Database has 73 sequences with 11270 residues. @@@@ cp -f tmp_2-b.mult /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.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 /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_2.a2m (71 sequences, 121 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 509169 \ -simple_threshold -14.8379305309692 -Emax 10 \ -adpstyle 1 \ -align_short 0 -mdEmax 10\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_2.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) .................. Average NLL-Simple NULL score: -8.597294 Database has 17012 sequences with 5858216 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_3-a.mult (36 sequences, 121 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=72 nll_thresh=-10.8379305309692 frac_id=0.854687107871842 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.854687107871842 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_3-a.train.seq (72 sequences, 121 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 5 (of 72) duplicate sequences with differing IDs Dropping 5 (of 72) duplicate sequences with identical IDs Dropping 56 (of 72) sequences with > 85.5% id 9 sequences left after dropping 63 of 72 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_3-a.train.seq (9 sequences, 121 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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -337.02 -53.43 -163.02 77.82 4 0 122 @@@@ 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 509169 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -14.8379305309692 -Emax 10 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.165289256198347 \ -align_short 5 -mdEmax 10 -constraints tmp_3-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_3.cst Reading parameter file tmp_3-b.mod tmp_3-b.mod(20): Reading MODEL -- Final model for run tmp_3-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -183.232941 Database has 75 sequences with 12016 residues. @@@@ cp -f tmp_3-b.mult /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_3.a2m @@@@ modelfromalign tmp_4-a -alignfile /projects/compbio/experiments/casp4/t98/T0098.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 /projects/compbio/experiments/casp4/t98/T0098.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_3.a2m (72 sequences, 121 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 509169 \ -simple_threshold -14.8379305309692 -Emax 10 \ -adpstyle 5 \ -align_short 0 -mdEmax 10\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.165289256198347 -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(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t98/T0098.remote-t2k_3.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) .................. Average NLL-Simple NULL score: -8.435469 Database has 17012 sequences with 5858216 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_4-a.mult (36 sequences, 121 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 /projects/compbio/experiments/casp4/t98/T0098.remote-t2k.a2m @@@@ cp tmp_4-a.train.cst /projects/compbio/experiments/casp4/t98/T0098.remote-t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-eclipse-7985 < /dev/null gzip -9f T0098.remote-t2k.a2m /projects/compbio/experiments/models.97/scripts99/score-target -alignment T0098.remote-t2k.a2m.gz -build w0.5 \ -db /projects/compbio/data/pdb/all-protein \ -Emax 40.0 \ -viterbi 0 -sw_score 2 \ -output T0098.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-4582 @@@@ mkdir /projects/compbio/tmp/score-target-4582/for-scorescript @@@@ /projects/compbio/experiments/models.97/scripts99/score-mods-vs-seqs.pl -root_tmp /projects/compbio/tmp/score-target-4582/for-scorescript -a2msfile /projects/compbio/tmp/score-target-4582/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-4582/score-target.op @@@@ chgrp protein /projects/compbio/tmp/score-target-4582/for-scorescript/split-tmp @@@@ chgrp protein /projects/compbio/tmp/score-target-4582/for-scorescript/split-tmp @@@@ /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/casp4/t98/T0098.remote-t2k.a2m.gz /projects/compbio/tmp/score-target-4582/for-scorescript/split-tmp/eclipse-31756/T0098.remote-t2k.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910/tmp -alignfile /projects/compbio/experiments/casp4/t98/T0098.remote-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/casp4/t98/T0098.remote-t2k.a2m.gz (72 sequences, 121 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910/tmp.a2m. Dropping 4 (of 72) duplicate sequences with differing IDs Dropping 4 (of 72) duplicate sequences with identical IDs Dropping 35 (of 72) sequences with > 80.0% id 8 sequences left after dropping 64 of 72 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910/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-eclipse-8910/tmp.a2m (8 sequences, 121 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910/tmp.mod /projects/compbio/tmp/score-target-4582/for-scorescript/split-tmp/eclipse-31756/T0098.remote-t2k.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8910 tmp.script echo ReadA2M T0098.t2k.a2m.gz >> tmp.script echo PrintPrediction T0098.t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0098.t2k.2d.seq >> tmp.script echo PrintRDB T0098.t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net # command:# Reading A2M format from T0098.t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0098.t2k.a2m with 36 sequences, total weight= 3.50994 avg weight= 0.0974983 11 iterations Regularizing alignment for T0098.t2k.a2m.gz # After reading T0098.t2k.a2m.gz, have 121 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0098.t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0098.t2k.2d.seq # command:# Network initialization done # Printing prediction to T0098.t2k.2d.rdb # command:rm tmp.script /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0098.t2k.2d.rdb T0098-t2k-2d.mod hmmscore T0098-t2k-2track \ -trackmod T0098.t2k-w0.5.mod,T0098-t2k-2d.mod \ -db /projects/compbio/experiments/test-set/fold-recognition-test/fssp-test-00/fssp-in-scop.seqs,/projects/compbio/experiments/test-set/fold-recognition-test/fssp-test-00/fssp-in-scop.2ds \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -dpstyle 0 \ -select_score 4 -Emax 40. SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098-t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) .. Average NLL-Simple NULL score: -10.821571 Database has 1997 sequences with 465801 residues. rm T0098-t2k-2d.mod