Multiple rules lines for `%.seq.gz' make -k PRED=1u9aA PRED2=1u joint Multiple rules lines for `%.seq.gz' Don't know how to make /projects/compbio/experiments/models.97/pdb/1u/1u9aA/struct-align/1u9aA.fssp.a2m /projects/compbio/experiments/models.97/scripts2k/target2k -out 1u9aA.fssp-w0.5.t2k -seed -all *** Error: /projects/compbio/experiments/models.97/scripts2k/target2k: /projects/compbio/experiments/casp4/t105/-all doesn't exist *** Exit 2 Don't know how to make /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99.a2m Don't know how to make yyy/xxxx.a2m `joint' not remade because of errors make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' mkdir 1u9aA fixmode 1u9aA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/1u9aA-T0105-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1u/1u9aA/struct-align/1u9aA.fssp-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1u9aA/struct-align/1u9aA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1u/1u9aA/struct-align/1u9aA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20009/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -111.972038 Database has 3 sequences with 414 residues. gzip -f 1u9aA/1u9aA-T0105-fssp-global.pw.a2m /projects/compbio/experiments/models.97/scripts2k/target2k -out T0105.t2k \ -seed T0105.seq \ -all @@@@ chgrp protein /projects/compbio/tmp/target2k-eclipse-10552 @@@@ cp /projects/compbio/experiments/casp4/t105/T0105.seq m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.2 (June, 2000) compiled 07/06/00_15:43:49 # 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= 517398 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-2670 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /projects/compbio/tmp/target2k-eclipse-10552/prefilter_1.fa, 0.01 For /projects/compbio/tmp/target2k-eclipse-10552/prefilter_2.fa, 1 For /projects/compbio/tmp/target2k-eclipse-10552/prefilter_3.fa, 10 For /projects/compbio/tmp/target2k-eclipse-10552/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-10552/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/tmp/target2k-eclipse-10552/m0.a2m (1 sequences, 94 columns) as A2M alignment. Writing sequence output to init.a2m. No sequences have been dropped. @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta E=400 V=20000 B=0 -gi > 1.fasta-blast.out Searched 517398 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-2670 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file m0.a2m (1 sequences, 94 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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file m0.a2m (1 sequences, 94 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 517398 \ -simple_threshold -26.3669080550283 -Emax 0.0001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.212765957446809 -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 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.162514 Database has 57 sequences with 28130 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.2 (June, 2000) compiled 07/06/00_15:43:43 Reading alignment file tmp_1-a.mult (31 sequences, 94 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=32 nll_thresh=-22.3669080550283 frac_id=0.999263589798278 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.999263589798278 -a2mdots 0 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file tmp_1-a.train.seq (32 sequences, 94 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 10 (of 32) duplicate sequences with differing IDs Dropping 1 (of 32) sequences with > 99.9% id 21 sequences left after dropping 11 of 32 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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file tmp_1-a.train.seq (21 sequences, 94 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 (June, 2000) compiled 07/07/00_22:42:24 -267.84 5.21 -98.26 51.69 8 0 95 @@@@ 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 517398 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -26.3669080550283 -Emax 0.0001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.212765957446809 \ -align_short 5 -mdEmax 0.0001 -constraints tmp_1-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t105/T0105.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 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -98.913086 Database has 44 sequences with 21378 residues. @@@@ cp -f tmp_1-b.mult /projects/compbio/experiments/casp4/t105/T0105.t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /projects/compbio/experiments/casp4/t105/T0105.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/t105/T0105.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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/experiments/casp4/t105/T0105.t2k_1.a2m (44 sequences, 94 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 517398 \ -simple_threshold -25.673760874275 -Emax 0.0002 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0002\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.212765957446809 -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 /projects/compbio/experiments/casp4/t105/T0105.t2k_1.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -71.250671 Database has 64 sequences with 29942 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.2 (June, 2000) compiled 07/06/00_15:43:43 Reading alignment file tmp_2-a.mult (44 sequences, 94 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=45 nll_thresh=-21.673760874275 frac_id=0.993575254183493 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.993575254183493 -a2mdots 0 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file tmp_2-a.train.seq (45 sequences, 94 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 18 (of 45) duplicate sequences with differing IDs 27 sequences left after dropping 18 of 45 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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file tmp_2-a.train.seq (27 sequences, 94 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 /projects/compbio/experiments/casp4/t105/T0105.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 (June, 2000) compiled 07/07/00_22:42:24 -266.47 -32.62 -92.04 41.79 5 0 95 @@@@ 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 517398 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -25.673760874275 -Emax 0.0002 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.212765957446809 \ -align_short 5 -mdEmax 0.0002 -constraints tmp_2-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t105/T0105.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 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -95.797363 Database has 45 sequences with 21750 residues. @@@@ cp -f tmp_2-b.mult /projects/compbio/experiments/casp4/t105/T0105.t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /projects/compbio/experiments/casp4/t105/T0105.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/t105/T0105.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 v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/experiments/casp4/t105/T0105.t2k_2.a2m (45 sequences, 94 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 517398 \ -simple_threshold -24.0643229602947 -Emax 0.001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.212765957446809 -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 /projects/compbio/experiments/casp4/t105/T0105.t2k_2.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -60.942398 Database has 72 sequences with 32007 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.2 (June, 2000) compiled 07/06/00_15:43:43 Reading alignment file tmp_3-a.mult (44 sequences, 94 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=45 nll_thresh=-20.0643229602947 frac_id=0.990844426375513 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.990844426375513 -a2mdots 0 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file tmp_3-a.train.seq (45 sequences, 94 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 18 (of 45) duplicate sequences with differing IDs 27 sequences left after dropping 18 of 45 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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file tmp_3-a.train.seq (27 sequences, 94 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(21): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t105/T0105.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 v3.2 (June, 2000) compiled 07/07/00_22:42:24 -266.47 -30.05 -87.12 41.78 4 0 95 @@@@ 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 517398 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -24.0643229602947 -Emax 0.001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.212765957446809 \ -align_short 5 -mdEmax 0.001 -constraints tmp_3-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t105/T0105.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 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -90.581367 Database has 45 sequences with 21750 residues. @@@@ cp -f tmp_3-b.mult /projects/compbio/experiments/casp4/t105/T0105.t2k_3.a2m # About to count sequences in prefilter_4.fa @@@@ modelfromalign tmp_4-a -alignfile /projects/compbio/experiments/casp4/t105/T0105.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/t105/T0105.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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/experiments/casp4/t105/T0105.t2k_3.a2m (45 sequences, 94 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 517398 \ -simple_threshold -22.4548850401296 -Emax 0.005 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.212765957446809 -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(21): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t105/T0105.t2k_3.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -17.703157 Database has 368 sequences with 103222 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.2 (June, 2000) compiled 07/06/00_15:43:43 Reading alignment file tmp_4-a.mult (44 sequences, 94 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=45 nll_thresh=-18.4548850401296 frac_id=0.986971920314047 @@@@ uniqueseq thinned_tmp -alignfile tmp_4-a.train.seq -a protein \ -percent_id 0.986971920314047 -a2mdots 0 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file tmp_4-a.train.seq (45 sequences, 94 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 18 (of 45) duplicate sequences with differing IDs Dropping 2 (of 45) sequences with > 98.7% id 25 sequences left after dropping 20 of 45 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 v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file tmp_4-a.train.seq (25 sequences, 94 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(21): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t105/T0105.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 v3.2 (June, 2000) compiled 07/07/00_22:42:24 -266.86 -29.03 -83.97 42.73 5 0 95 @@@@ 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 517398 \ -db m0.a2m -db tmp_4-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -22.4548850401296 -Emax 0.005 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.212765957446809 \ -align_short 5 -mdEmax 0.005 -constraints tmp_4-a.train.cst -constraints_out /projects/compbio/experiments/casp4/t105/T0105.t2k_4.cst Reading parameter file tmp_4-b.mod tmp_4-b.mod(18): Reading MODEL -- Final model for run tmp_4-b SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -74.024994 Database has 57 sequences with 27536 residues. @@@@ cp -f tmp_4-b.mult /projects/compbio/experiments/casp4/t105/T0105.t2k_4.a2m @@@@ modelfromalign tmp_5-a -alignfile /projects/compbio/experiments/casp4/t105/T0105.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/t105/T0105.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 v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/experiments/casp4/t105/T0105.t2k_4.a2m (57 sequences, 94 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 517398 \ -simple_threshold -22.4548850401296 -Emax 0.005 \ -adpstyle 5 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.212765957446809 -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(21): Reading MODEL -- Model from alignment file /projects/compbio/experiments/casp4/t105/T0105.t2k_4.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -18.556078 Database has 368 sequences with 103222 residues. @@@@ sortseq tmp_5-a-sort -alignfile tmp_5-a.mult \ -NLLfile tmp_5-a.mstat -a2mdots 0 SAM: sortseq v3.2 (June, 2000) compiled 07/06/00_15:43:43 Reading alignment file tmp_5-a.mult (56 sequences, 94 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/t105/T0105.t2k.a2m @@@@ cp tmp_5-a.train.cst /projects/compbio/experiments/casp4/t105/T0105.t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-eclipse-10552 < /dev/null gzip -f T0105.t2k.a2m T0105.t2k_*.a2m /projects/compbio/bin/scripts/w0.5 T0105.t2k.a2m.gz T0105.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp -alignfile T0105.t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file T0105.t2k.a2m.gz (57 sequences, 94 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m. Dropping 29 (of 57) duplicate sequences with differing IDs Dropping 15 (of 57) sequences with > 80.0% id 13 sequences left after dropping 44 of 57 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m (13 sequences, 94 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.mod T0105.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-local.pw -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.007130 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-local.pw.a2m make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/1u9aA-T0105-local.pw -i /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9065/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -99.050140 Database has 3 sequences with 414 residues. gzip -f 1u9aA/1u9aA-T0105-local.pw.a2m make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-vit.pw \ -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -39.349133 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-vit.pw.a2m make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/1u9aA-T0105-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9065/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -95.623138 Database has 3 sequences with 414 residues. gzip -f 1u9aA/1u9aA-T0105-vit.pw.a2m make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-global.pw -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -24.198685 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-global.pw.a2m make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/1u9aA-T0105-global.pw -i /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1u/1u9aA/nostruct-align/1u9aA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9065/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -94.173676 Database has 3 sequences with 414 residues. gzip -f 1u9aA/1u9aA-T0105-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' mkdir 1tie fixmode 1tie make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-local.pw -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.307758 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-local.pw.a2m make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/1tie-T0105-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12319/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -99.845741 Database has 3 sequences with 432 residues. gzip -f 1tie/1tie-T0105-local.pw.a2m make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-vit.pw \ -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -38.238079 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-vit.pw.a2m make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/1tie-T0105-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12319/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -96.170753 Database has 3 sequences with 432 residues. gzip -f 1tie/1tie-T0105-vit.pw.a2m make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-global.pw -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -17.525660 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-global.pw.a2m make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/1tie-T0105-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tie/nostruct-align/1tie.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12319/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -94.431030 Database has 3 sequences with 432 residues. gzip -f 1tie/1tie-T0105-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp.a2m.gz (19 sequences, 171 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/tmp.a2m. Dropping 1 (of 19) duplicate sequences with differing IDs Dropping 5 (of 19) sequences with > 80.0% id 13 sequences left after dropping 6 of 19 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/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 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/tmp.a2m (13 sequences, 171 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/tmp.mod /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' mkdir 1wba fixmode 1wba make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/1wba-T0105-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1w/1wba/struct-align/1wba.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12580/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -88.586342 Database has 3 sequences with 440 residues. gzip -f 1wba/1wba-T0105-fssp-global.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-local.pw -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -37.193756 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-local.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/1wba-T0105-local.pw -i /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-32429/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -90.689423 Database has 3 sequences with 440 residues. gzip -f 1wba/1wba-T0105-local.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-vit.pw \ -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -32.485096 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-vit.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/1wba-T0105-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-32429/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -87.113426 Database has 3 sequences with 440 residues. gzip -f 1wba/1wba-T0105-vit.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-global.pw -i T0105.t2k-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0105.t2k-w0.5.mod T0105.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -16.971014 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-global.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/1wba-T0105-global.pw -i /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod -db T0105.seq -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1w/1wba/nostruct-align/1wba.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-32429/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -83.651695 Database has 3 sequences with 440 residues. gzip -f 1wba/1wba-T0105-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0105.t2k.2d.rdb T0105.t2k-2d.mod make 1u9aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1u9aA Error in locating FIM delete in 1u9aA . Average NLL-Simple NULL score: -34.426296 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1tie Error in locating FIM delete in 1tie . Average NLL-Simple NULL score: -32.219418 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1wba make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1wba Error in locating FIM delete in 1wba . Average NLL-Simple NULL score: -32.291767 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1u9aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -34.426296 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -32.219418 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1wba make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -32.291767 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1u9aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -34.426296 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -32.219418 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1wba make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -32.291767 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1u9aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1718.852417 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1909.200806 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1wba make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2047.036255 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1u9aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -3733.080322 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-local.pw.a2m make 1u9aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -3723.181396 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -3718.215576 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-local.pw.a2m make 1tie make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -3706.463623 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make 1wba make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -3716.759033 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-local.pw.a2m make 1wba make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0105.t2k-2d.mod(587): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -3703.919922 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1u9aA PRED2=1u joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(593): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -34.046474 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-local.pw.a2m make 1u9aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1u9aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1u9aA/T0105-1u9aA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1u/1u9aA/info/1u9aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(593): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -21.254356 Database has 3 sequences with 414 residues. gzip -f 1u9aA/T0105-1u9aA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1u9aA/xxxx-1u9aA-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1tie PRED2=1t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1t/1tie/struct-align/1tie.fssp-w0.5.mod', needed by `1tie/1tie-T0105-fssp-global.pw.a2m.gz'. make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(593): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -33.848251 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-local.pw.a2m make 1tie make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1tie' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1tie/T0105-1tie-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tie/info/1tie.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(593): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -4.938509 Database has 3 sequences with 432 residues. gzip -f 1tie/T0105-1tie-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tie/xxxx-1tie-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1wba PRED2=1w joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(593): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -33.863094 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-local.pw.a2m make 1wba make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' make[2]: `1wba' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' hmmscore 1wba/T0105-1wba-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0105.t2k-w0.5.mod,T0105.t2k-2d.mod \ -db T0105.seq,T0105.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.seq,/projects/compbio/experiments/models.97/pdb/1w/1wba/info/1wba.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0105.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14311/tmp.a2m T0105.t2k-2d.mod(593): Reading track 1 model from MODEL -- Model from 2nd structure file T0105.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -5.324679 Database has 3 sequences with 440 residues. gzip -f 1wba/T0105-1wba-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1wba/xxxx-1wba-T0105-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t105' make: [joints] Error 2 (ignored) make -k PRED=1a3qA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t105' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a3qA/struct-align/1a3qA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a3qA/struct-align/1a3qA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-10067 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-10067/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a3qA/struct-align/1a3qA.fssp.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 /projects/compbio/experiments/models.97/pdb/1a/1a3qA/struct-align/1a3qA.fssp.a2m.gz (24 sequences, 285 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-10067/tmp.a2m. Dropping 8 (of 24) duplicate sequences with differing IDs Dropping 6 (of 24) sequences with > 80.0% id 10 sequences left after dropping 14 of 24 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-10067/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-10067/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-purr-10067/tmp.a2m (10 sequences, 285 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-10067/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a3qA/struct-align/1a3qA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-purr-10067