make -k PRED=1dquA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dquA/struct-align/1dquA.fssp-w0.5.mod', needed by `1dquA/1dquA-T0108-fssp-global.pw.a2m.gz'. /projects/compbio/bin/scripts/w0.5 T0108.t2k.a2m.gz T0108.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp -alignfile T0108.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 T0108.t2k.a2m.gz (19 sequences, 206 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m. Dropping 3 (of 19) duplicate sequences with differing IDs Dropping 5 (of 19) sequences with > 80.0% id 11 sequences left after dropping 8 of 19 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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-8236/tmp.a2m (11 sequences, 206 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.mod T0108.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1dquA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 1dquA fixmode 1dquA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -81.956726 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-local.pw.a2m make 1dquA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/1dquA-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5178/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -352.647736 Database has 3 sequences with 1257 residues. gzip -f 1dquA/1dquA-T0108-local.pw.a2m make 1dquA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -78.506409 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-vit.pw.a2m make 1dquA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/1dquA-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5178/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -349.471405 Database has 3 sequences with 1257 residues. gzip -f 1dquA/1dquA-T0108-vit.pw.a2m make 1dquA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -16.535696 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-global.pw.a2m make 1dquA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/1dquA-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dquA/nostruct-align/1dquA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5178/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: -342.440704 Database has 3 sequences with 1257 residues. gzip -f 1dquA/1dquA-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dquA/xxxx-1dquA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1gtrA PRED2=1g joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.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/1g/1gtrA/struct-align/1gtrA.fssp.a2m.gz (17 sequences, 529 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498/tmp.a2m. Dropping 2 (of 17) duplicate sequences with differing IDs Dropping 4 (of 17) sequences with > 80.0% id 11 sequences left after dropping 6 of 17 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498/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-9498/tmp.a2m (11 sequences, 529 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498/tmp.mod /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 1gtrA fixmode 1gtrA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/1gtrA-T0108-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.fssp-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gtrA/struct-align/1gtrA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9498/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: -352.426361 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/1gtrA-T0108-fssp-global.pw.a2m make 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -82.417053 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-local.pw.a2m make 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/1gtrA-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4526/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -327.596710 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/1gtrA-T0108-local.pw.a2m make 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -76.593040 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-vit.pw.a2m make 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/1gtrA-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4526/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -323.716675 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/1gtrA-T0108-vit.pw.a2m make 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -20.027029 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-global.pw.a2m make 1gtrA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/1gtrA-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gtrA/nostruct-align/1gtrA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4526/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: -314.228729 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/1gtrA-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gtrA/xxxx-1gtrA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1lt3A PRED2=1l joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.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/1l/1lt3A/struct-align/1lt3A.fssp.a2m.gz (12 sequences, 226 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641/tmp.a2m. Dropping 3 (of 12) duplicate sequences with differing IDs Dropping 6 (of 12) sequences with > 80.0% id 3 sequences left after dropping 9 of 12 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641/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-4641/tmp.a2m (3 sequences, 226 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641/tmp.mod /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 1lt3A fixmode 1lt3A make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/1lt3A-T0108-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.fssp-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lt3A/struct-align/1lt3A.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4641/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: -201.682007 Database has 3 sequences with 672 residues. gzip -f 1lt3A/1lt3A-T0108-fssp-global.pw.a2m make 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -79.337669 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-local.pw.a2m make 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/1lt3A-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14193/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -211.663681 Database has 3 sequences with 672 residues. gzip -f 1lt3A/1lt3A-T0108-local.pw.a2m make 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -72.847328 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-vit.pw.a2m make 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/1lt3A-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14193/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -208.469360 Database has 3 sequences with 672 residues. gzip -f 1lt3A/1lt3A-T0108-vit.pw.a2m make 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -65.723030 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-global.pw.a2m make 1lt3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/1lt3A-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lt3A/nostruct-align/1lt3A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14193/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: -205.507690 Database has 3 sequences with 672 residues. gzip -f 1lt3A/1lt3A-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lt3A/xxxx-1lt3A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1abrB PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.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/1a/1abrB/struct-align/1abrB.fssp.a2m.gz (13 sequences, 267 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719/tmp.a2m. Dropping 1 (of 13) duplicate sequences with differing IDs 12 sequences left after dropping 1 of 13 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719/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-2719/tmp.a2m (12 sequences, 267 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 1abrB fixmode 1abrB make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.fssp-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/struct-align/1abrB.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2719/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: -187.339050 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-fssp-global.pw.a2m make 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -79.255959 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-local.pw.a2m make 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14409/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -169.513596 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-local.pw.a2m make 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -73.236267 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-vit.pw.a2m make 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14409/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -165.595947 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-vit.pw.a2m make 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -59.667042 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-global.pw.a2m make 1abrB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14409/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: -166.154037 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abrB/xxxx-1abrB-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1cs8A PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.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/1c/1cs8A/struct-align/1cs8A.fssp.a2m.gz (56 sequences, 316 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889/tmp.a2m. Dropping 28 (of 56) duplicate sequences with differing IDs Dropping 14 (of 56) sequences with > 80.0% id 14 sequences left after dropping 42 of 56 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889/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-7889/tmp.a2m (14 sequences, 316 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 1cs8A fixmode 1cs8A make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/1cs8A-T0108-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.fssp-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cs8A/struct-align/1cs8A.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7889/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: -224.745712 Database has 3 sequences with 838 residues. gzip -f 1cs8A/1cs8A-T0108-fssp-global.pw.a2m make 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -76.858253 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-local.pw.a2m make 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/1cs8A-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file ./tmp/tmp-build-weighted-model-alpha-6366/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -201.285263 Database has 3 sequences with 838 residues. gzip -f 1cs8A/1cs8A-T0108-local.pw.a2m make 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -72.063904 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-vit.pw.a2m make 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/1cs8A-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file ./tmp/tmp-build-weighted-model-alpha-6366/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -197.487244 Database has 3 sequences with 838 residues. gzip -f 1cs8A/1cs8A-T0108-vit.pw.a2m make 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -49.183033 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-global.pw.a2m make 1cs8A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/1cs8A-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cs8A/nostruct-align/1cs8A.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file ./tmp/tmp-build-weighted-model-alpha-6366/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: -195.085709 Database has 3 sequences with 838 residues. gzip -f 1cs8A/1cs8A-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cs8A/xxxx-1cs8A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1d7qA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.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/1d/1d7qA/struct-align/1d7qA.fssp.a2m.gz (1 sequences, 143 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991/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-5991/tmp.a2m (1 sequences, 143 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991/tmp.mod /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 1d7qA fixmode 1d7qA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/1d7qA-T0108-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.fssp-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1d7qA/struct-align/1d7qA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5991/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: -142.328690 Database has 3 sequences with 492 residues. gzip -f 1d7qA/1d7qA-T0108-fssp-global.pw.a2m make 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -80.936829 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-local.pw.a2m make 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/1d7qA-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16566/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -101.453163 Database has 3 sequences with 492 residues. gzip -f 1d7qA/1d7qA-T0108-local.pw.a2m make 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -77.147156 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-vit.pw.a2m make 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/1d7qA-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16566/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -99.087158 Database has 3 sequences with 492 residues. gzip -f 1d7qA/1d7qA-T0108-vit.pw.a2m make 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -71.532341 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-global.pw.a2m make 1d7qA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/1d7qA-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1d7qA/nostruct-align/1d7qA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16566/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: -94.973694 Database has 3 sequences with 492 residues. gzip -f 1d7qA/1d7qA-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d7qA/xxxx-1d7qA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=16pk PRED2=16 joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608/tmp -alignfile /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.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/16/16pk/struct-align/16pk.fssp.a2m.gz (13 sequences, 415 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608/tmp.a2m. Dropping 4 (of 13) duplicate sequences with differing IDs Dropping 1 (of 13) sequences with > 80.0% id 8 sequences left after dropping 5 of 13 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608/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-7608/tmp.a2m (8 sequences, 415 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608/tmp.mod /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' mkdir 16pk fixmode 16pk make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/16pk-T0108-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.fssp-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/16/16pk/struct-align/16pk.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7608/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: -293.423706 Database has 3 sequences with 1036 residues. gzip -f 16pk/16pk-T0108-fssp-global.pw.a2m make 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-local.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -77.678566 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-local.pw.a2m make 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/16pk-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29881/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -270.604553 Database has 3 sequences with 1036 residues. gzip -f 16pk/16pk-T0108-local.pw.a2m make 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-vit.pw \ -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -74.272278 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-vit.pw.a2m make 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/16pk-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29881/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -266.956879 Database has 3 sequences with 1036 residues. gzip -f 16pk/16pk-T0108-vit.pw.a2m make 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-global.pw -i T0108.t2k-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0108.t2k-w0.5.mod T0108.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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: -37.657032 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-global.pw.a2m make 16pk make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' hmmscore 16pk/16pk-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/16/16pk/nostruct-align/16pk.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29881/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: -260.988068 Database has 3 sequences with 1036 residues. gzip -f 16pk/16pk-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `16pk/xxxx-16pk-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1dquA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dquA/struct-align/1dquA.fssp-w0.5.mod', needed by `1dquA/1dquA-T0108-fssp-global.pw.a2m.gz'. /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0108.t2k.2d.rdb T0108.t2k-2d.mod make 1dquA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1dquA Error in locating FIM delete in 1dquA . Average NLL-Simple NULL score: -62.523026 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dquA/xxxx-1dquA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1gtrA PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1gtrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1gtrA Error in locating FIM delete in 1gtrA . Average NLL-Simple NULL score: -62.503819 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gtrA/xxxx-1gtrA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1lt3A PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1lt3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.128006 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lt3A/xxxx-1lt3A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1abrB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12094/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -169.764603 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-local.pw.a2m make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.110592 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-2track-local.pw.a2m make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12094/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -166.165588 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-vit.pw.a2m make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/1abrB-T0108-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod -db T0108.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1abrB/nostruct-align/1abrB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12094/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 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: -165.066040 Database has 3 sequences with 740 residues. gzip -f 1abrB/1abrB-T0108-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abrB/xxxx-1abrB-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1cs8A PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1cs8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.093582 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cs8A/xxxx-1cs8A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1d7qA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1d7qA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.747837 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d7qA/xxxx-1d7qA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=16pk PRED2=16 joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 16pk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.858231 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `16pk/xxxx-16pk-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1dquA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dquA/struct-align/1dquA.fssp-w0.5.mod', needed by `1dquA/1dquA-T0108-fssp-global.pw.a2m.gz'. make 1dquA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.523026 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dquA/xxxx-1dquA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1gtrA PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1gtrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.503819 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gtrA/xxxx-1gtrA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1lt3A PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1lt3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.128006 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lt3A/xxxx-1lt3A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1abrB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.110592 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abrB/xxxx-1abrB-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1cs8A PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1cs8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.093582 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cs8A/xxxx-1cs8A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1d7qA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1d7qA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.747837 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d7qA/xxxx-1d7qA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=16pk PRED2=16 joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 16pk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.858231 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `16pk/xxxx-16pk-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1dquA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dquA/struct-align/1dquA.fssp-w0.5.mod', needed by `1dquA/1dquA-T0108-fssp-global.pw.a2m.gz'. make 1dquA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.523026 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dquA/xxxx-1dquA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1gtrA PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1gtrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.503819 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gtrA/xxxx-1gtrA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1lt3A PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1lt3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.128006 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lt3A/xxxx-1lt3A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1abrB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.110592 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abrB/xxxx-1abrB-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1cs8A PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1cs8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.093582 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cs8A/xxxx-1cs8A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1d7qA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1d7qA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.747837 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d7qA/xxxx-1d7qA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=16pk PRED2=16 joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 16pk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.858231 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `16pk/xxxx-16pk-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1dquA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dquA/struct-align/1dquA.fssp-w0.5.mod', needed by `1dquA/1dquA-T0108-fssp-global.pw.a2m.gz'. make 1dquA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 8020.492676 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dquA/xxxx-1dquA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1gtrA PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1gtrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 8477.614258 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gtrA/xxxx-1gtrA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1lt3A PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1lt3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 694.527344 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lt3A/xxxx-1lt3A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1abrB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1576.336060 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abrB/xxxx-1abrB-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1cs8A PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1cs8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2851.004150 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cs8A/xxxx-1cs8A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1d7qA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1d7qA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -39.318344 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d7qA/xxxx-1d7qA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=16pk PRED2=16 joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 16pk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/tmp.a2m T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 5454.331543 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `16pk/xxxx-16pk-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1dquA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dquA/struct-align/1dquA.fssp-w0.5.mod', needed by `1dquA/1dquA-T0108-fssp-global.pw.a2m.gz'. make 1dquA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8137.582031 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-2track-local.pw.a2m make 1dquA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1dquA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1dquA/T0108-1dquA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dquA/info/1dquA.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8101.096191 Database has 3 sequences with 1257 residues. gzip -f 1dquA/T0108-1dquA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dquA/xxxx-1dquA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1gtrA PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1gtrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8167.882812 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-2track-local.pw.a2m make 1gtrA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1gtrA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1gtrA/T0108-1gtrA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtrA/info/1gtrA.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8116.683594 Database has 3 sequences with 1288 residues. gzip -f 1gtrA/T0108-1gtrA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gtrA/xxxx-1gtrA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1lt3A PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1lt3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8126.688965 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-2track-local.pw.a2m make 1lt3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1lt3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1lt3A/T0108-1lt3A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lt3A/info/1lt3A.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8126.460937 Database has 3 sequences with 672 residues. gzip -f 1lt3A/T0108-1lt3A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lt3A/xxxx-1lt3A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1abrB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8178.256348 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-2track-local.pw.a2m make 1abrB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1abrB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1abrB/T0108-1abrB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abrB/info/1abrB.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8173.880371 Database has 3 sequences with 740 residues. gzip -f 1abrB/T0108-1abrB-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abrB/xxxx-1abrB-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1cs8A PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1cs8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8165.136719 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-2track-local.pw.a2m make 1cs8A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1cs8A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1cs8A/T0108-1cs8A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cs8A/info/1cs8A.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8152.307129 Database has 3 sequences with 838 residues. gzip -f 1cs8A/T0108-1cs8A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cs8A/xxxx-1cs8A-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=1d7qA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 1d7qA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -6532.604004 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-2track-local.pw.a2m make 1d7qA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `1d7qA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 1d7qA/T0108-1d7qA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d7qA/info/1d7qA.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -6529.213379 Database has 3 sequences with 492 residues. gzip -f 1d7qA/T0108-1d7qA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d7qA/xxxx-1d7qA-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored) make -k PRED=16pk PRED2=16 joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make 16pk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.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 T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8144.578125 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-2track-local.pw.a2m make 16pk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t108' make[2]: `16pk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' hmmscore 16pk/T0108-16pk-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0108.t2k-w0.5.mod,T0108.t2k-2d.mod \ -db T0108.seq,T0108.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.stride.seq,/projects/compbio/experiments/models.97/pdb/16/16pk/info/16pk.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. T0108.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8236/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. T0108.t2k-2d.mod(1259): Reading track 1 model from MODEL -- Model from 2nd structure file T0108.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: -8124.341309 Database has 3 sequences with 1036 residues. gzip -f 16pk/T0108-16pk-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `16pk/xxxx-16pk-T0108-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t108' make: [joints] Error 2 (ignored)