make -k PRED=1eaiC PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1eaiC/struct-align/1eaiC.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1eaiC/struct-align/1eaiC.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 1eaiC fixmode 1eaiC make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/1eaiC-T0106-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eaiC/struct-align/1eaiC.fssp-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/1eaiC-T0106-fssp-global.pw.a2m /projects/compbio/bin/scripts/w0.5 T0106.t2k.a2m.gz T0106.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1eaiC' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/T0106-1eaiC-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/T0106-1eaiC-local.pw.a2m make 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1eaiC' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/1eaiC-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eaiC/nostruct-align/1eaiC.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/1eaiC-T0106-local.pw.a2m make 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1eaiC' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/T0106-1eaiC-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/T0106-1eaiC-vit.pw.a2m make 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1eaiC' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/1eaiC-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1eaiC/nostruct-align/1eaiC.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/1eaiC-T0106-vit.pw.a2m make 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1eaiC' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/T0106-1eaiC-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/T0106-1eaiC-global.pw.a2m make 1eaiC make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1eaiC' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1eaiC/1eaiC-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eaiC/nostruct-align/1eaiC.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eaiC/info/1eaiC.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eaiC/1eaiC-T0106-global.pw.a2m make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make -k PRED=1eaiC PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eaiC/xxxx-1eaiC-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored) make -k PRED=1dqgA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dqgA/struct-align/1dqgA.fssp-w0.5.mod', needed by `1dqgA/1dqgA-T0106-fssp-global.pw.a2m.gz'. make 1dqgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 1dqgA fixmode 1dqgA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1dqgA/T0106-1dqgA-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -46.050976 Database has 3 sequences with 397 residues. gzip -f 1dqgA/T0106-1dqgA-local.pw.a2m make 1dqgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1dqgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1dqgA/1dqgA-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3641/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -91.053642 Database has 3 sequences with 397 residues. gzip -f 1dqgA/1dqgA-T0106-local.pw.a2m make 1dqgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1dqgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1dqgA/T0106-1dqgA-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -41.964966 Database has 3 sequences with 397 residues. gzip -f 1dqgA/T0106-1dqgA-vit.pw.a2m make 1dqgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1dqgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1dqgA/1dqgA-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3641/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -88.288643 Database has 3 sequences with 397 residues. gzip -f 1dqgA/1dqgA-T0106-vit.pw.a2m make 1dqgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1dqgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1dqgA/T0106-1dqgA-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -86.352356 Database has 3 sequences with 397 residues. gzip -f 1dqgA/T0106-1dqgA-global.pw.a2m make 1dqgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1dqgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1dqgA/1dqgA-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dqgA/info/1dqgA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dqgA/nostruct-align/1dqgA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-3641/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -87.205353 Database has 3 sequences with 397 residues. gzip -f 1dqgA/1dqgA-T0106-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dqgA/xxxx-1dqgA-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored) make -k PRED=1by2 PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1by2/struct-align/1by2.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1by2/struct-align/1by2.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-19651 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-19651/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1by2/struct-align/1by2.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /projects/compbio/experiments/models.97/pdb/1b/1by2/struct-align/1by2.fssp.a2m.gz (1 sequences, 112 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-19651/tmp.a2m. No sequences have been droppd. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-19651/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-19651/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-19651/tmp.a2m (1 sequences, 112 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-19651/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1by2/struct-align/1by2.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-purr-19651 80.0% id 10 sequences left after dropping 21 of 31 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-29020/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-29020/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-29020/tmp.a2m (10 sequences, 84 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-29020/tmp.mod /projects/compbio/experiments/models.97/pdb/5h/5hpgA/struct-align/5hpgA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 5hpgA fixmode 5hpgA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/5hpgA-T0106-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/5h/5hpgA/struct-align/5hpgA.fssp-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5h/5hpgA/struct-align/5hpgA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/5h/5hpgA/struct-align/5hpgA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-29020/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: -64.346344 Database has 3 sequences with 296 residues. gzip -f 5hpgA/5hpgA-T0106-fssp-global.pw.a2m make 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `5hpgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/T0106-5hpgA-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.750469 Database has 3 sequences with 296 residues. gzip -f 5hpgA/T0106-5hpgA-local.pw.a2m make 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `5hpgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/5hpgA-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4936/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.173462 Database has 3 sequences with 296 residues. gzip -f 5hpgA/5hpgA-T0106-local.pw.a2m make 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `5hpgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/T0106-5hpgA-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.596130 Database has 3 sequences with 296 residues. gzip -f 5hpgA/T0106-5hpgA-vit.pw.a2m make 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `5hpgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/5hpgA-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4936/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -57.812458 Database has 3 sequences with 296 residues. gzip -f 5hpgA/5hpgA-T0106-vit.pw.a2m make 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `5hpgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/T0106-5hpgA-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/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: -32.240021 Database has 3 sequences with 296 residues. gzip -f 5hpgA/T0106-5hpgA-global.pw.a2m make 5hpgA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `5hpgA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 5hpgA/5hpgA-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5h/5hpgA/info/5hpgA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/5h/5hpgA/nostruct-align/5hpgA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4936/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: -58.650349 Database has 3 sequences with 296 residues. gzip -f 5hpgA/5hpgA-T0106-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5hpgA/xxxx-5hpgA-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored) make -k PRED=1boeA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.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/1b/1boeA/struct-align/1boeA.fssp.a2m.gz (2 sequences, 46 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022/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-5022/tmp.a2m (2 sequences, 46 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 1boeA fixmode 1boeA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/1boeA-T0106-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.fssp-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1boeA/struct-align/1boeA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-5022/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: -32.481014 Database has 3 sequences with 221 residues. gzip -f 1boeA/1boeA-T0106-fssp-global.pw.a2m make 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1boeA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/T0106-1boeA-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -45.814411 Database has 3 sequences with 221 residues. gzip -f 1boeA/T0106-1boeA-local.pw.a2m make 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1boeA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/1boeA-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7799/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -38.458740 Database has 3 sequences with 221 residues. gzip -f 1boeA/1boeA-T0106-local.pw.a2m make 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1boeA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/T0106-1boeA-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.563736 Database has 3 sequences with 221 residues. gzip -f 1boeA/T0106-1boeA-vit.pw.a2m make 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1boeA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/1boeA-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7799/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -35.588078 Database has 3 sequences with 221 residues. gzip -f 1boeA/1boeA-T0106-vit.pw.a2m make 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1boeA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/T0106-1boeA-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/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: -33.016682 Database has 3 sequences with 221 residues. gzip -f 1boeA/T0106-1boeA-global.pw.a2m make 1boeA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1boeA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1boeA/1boeA-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1boeA/info/1boeA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1boeA/nostruct-align/1boeA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7799/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: -34.213673 Database has 3 sequences with 221 residues. gzip -f 1boeA/1boeA-T0106-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1boeA/xxxx-1boeA-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored) make -k PRED=4htcI PRED2=4h joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946/tmp -alignfile /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.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/4h/4htcI/struct-align/4htcI.fssp.a2m.gz (8 sequences, 61 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946/tmp.a2m. Dropping 2 (of 8) duplicate sequences with differing IDs Dropping 5 (of 8) sequences with > 80.0% id 1 sequences left after dropping 7 of 8 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946/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-1946/tmp.a2m (1 sequences, 61 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946/tmp.mod /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 4htcI fixmode 4htcI make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/4htcI-T0106-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.fssp-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/4h/4htcI/struct-align/4htcI.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-1946/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: -56.554348 Database has 3 sequences with 254 residues. gzip -f 4htcI/4htcI-T0106-fssp-global.pw.a2m make 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `4htcI' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/T0106-4htcI-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.899918 Database has 3 sequences with 254 residues. gzip -f 4htcI/T0106-4htcI-local.pw.a2m make 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `4htcI' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/4htcI-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12140/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.118252 Database has 3 sequences with 254 residues. gzip -f 4htcI/4htcI-T0106-local.pw.a2m make 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `4htcI' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/T0106-4htcI-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.568249 Database has 3 sequences with 254 residues. gzip -f 4htcI/T0106-4htcI-vit.pw.a2m make 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `4htcI' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/4htcI-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12140/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.292912 Database has 3 sequences with 254 residues. gzip -f 4htcI/4htcI-T0106-vit.pw.a2m make 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `4htcI' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/T0106-4htcI-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/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: -33.496342 Database has 3 sequences with 254 residues. gzip -f 4htcI/T0106-4htcI-global.pw.a2m make 4htcI make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `4htcI' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 4htcI/4htcI-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/4h/4htcI/info/4htcI.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/4h/4htcI/nostruct-align/4htcI.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12140/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: -47.081345 Database has 3 sequences with 254 residues. gzip -f 4htcI/4htcI-T0106-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `4htcI/xxxx-4htcI-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored) make -k PRED=1c4eA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.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/1c4eA/struct-align/1c4eA.fssp.a2m.gz (2 sequences, 35 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483/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-7483/tmp.a2m (2 sequences, 35 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 1c4eA fixmode 1c4eA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/1c4eA-T0106-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.fssp-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1c4eA/struct-align/1c4eA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7483/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: -23.595675 Database has 3 sequences with 198 residues. gzip -f 1c4eA/1c4eA-T0106-fssp-global.pw.a2m make 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1c4eA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/T0106-1c4eA-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -46.838104 Database has 3 sequences with 198 residues. gzip -f 1c4eA/T0106-1c4eA-local.pw.a2m make 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1c4eA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/1c4eA-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2446/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.309765 Database has 3 sequences with 198 residues. gzip -f 1c4eA/1c4eA-T0106-local.pw.a2m make 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1c4eA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/T0106-1c4eA-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.755096 Database has 3 sequences with 198 residues. gzip -f 1c4eA/T0106-1c4eA-vit.pw.a2m make 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1c4eA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/1c4eA-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2446/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.737434 Database has 3 sequences with 198 residues. gzip -f 1c4eA/1c4eA-T0106-vit.pw.a2m make 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1c4eA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/T0106-1c4eA-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/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: -33.786678 Database has 3 sequences with 198 residues. gzip -f 1c4eA/T0106-1c4eA-global.pw.a2m make 1c4eA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1c4eA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1c4eA/1c4eA-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1c4eA/info/1c4eA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1c4eA/nostruct-align/1c4eA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2446/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: -31.991999 Database has 3 sequences with 198 residues. gzip -f 1c4eA/1c4eA-T0106-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c4eA/xxxx-1c4eA-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored) make -k PRED=1klo PRED2=1k joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.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/1k/1klo/struct-align/1klo.fssp.a2m.gz (2 sequences, 162 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336/tmp.a2m. Dropping 1 (of 2) sequences with > 80.0% id 1 sequences left after dropping 1 of 2 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336/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-10336/tmp.a2m (1 sequences, 162 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336/tmp.mod /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' mkdir 1klo fixmode 1klo make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/1klo-T0106-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.fssp-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1k/1klo/struct-align/1klo.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10336/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: -185.931686 Database has 3 sequences with 452 residues. gzip -f 1klo/1klo-T0106-fssp-global.pw.a2m make 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1klo' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/T0106-1klo-local.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.097950 Database has 3 sequences with 452 residues. gzip -f 1klo/T0106-1klo-local.pw.a2m make 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1klo' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/1klo-T0106-local.pw -i /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2641/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -88.333961 Database has 3 sequences with 452 residues. gzip -f 1klo/1klo-T0106-local.pw.a2m make 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1klo' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/T0106-1klo-vit.pw \ -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.830273 Database has 3 sequences with 452 residues. gzip -f 1klo/T0106-1klo-vit.pw.a2m make 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1klo' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/1klo-T0106-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2641/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -84.777283 Database has 3 sequences with 452 residues. gzip -f 1klo/1klo-T0106-vit.pw.a2m make 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1klo' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/T0106-1klo-global.pw -i T0106.t2k-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0106.t2k-w0.5.mod T0106.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-27231/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: -35.292675 Database has 3 sequences with 452 residues. gzip -f 1klo/T0106-1klo-global.pw.a2m make 1klo make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t106' make[2]: `1klo' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' hmmscore 1klo/1klo-T0106-global.pw -i /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod -db T0106.seq -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1klo/info/1klo.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1k/1klo/nostruct-align/1klo.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2641/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: -86.287682 Database has 3 sequences with 452 residues. gzip -f 1klo/1klo-T0106-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1klo/xxxx-1klo-T0106-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t106' make: [joints] Error 2 (ignored)