make -k PRED=2chsA PRED2=2c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2chsA/xxxx-2chsA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=5csmA PRED2=5c \ MODELBASE=5csmA/5csmA+1ecm MODELNAME=5csmA+1ecm joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: Nothing to be done for `joint'. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make -k PRED=5csmA PRED2=5c \ MODELBASE=5csmA/5csmA+1ecm.t2k-from-a2m \ MODELNAME=5csmA+1ecm.t2k joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: Nothing to be done for `joint'. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make -k PRED=1ecmA PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ecmA/xxxx-1ecmA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1sesA PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sesA/xxxx-1sesA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1auiA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1auiA/xxxx-1auiA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1bxnA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bxnA/struct-align/1bxnA.fssp-w0.5.mod', needed by `1bxnA/1bxnA-T0086-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t99-w0.5.mod', needed by `1bxnA/1bxnA-T0086-local.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxnA/xxxx-1bxnA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=2chsA PRED2=2c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2chsA/xxxx-2chsA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=5csmA PRED2=5c \ MODELBASE=5csmA/5csmA+1ecm MODELNAME=5csmA+1ecm joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: Nothing to be done for `joint'. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make -k PRED=5csmA PRED2=5c \ MODELBASE=5csmA/5csmA+1ecm.t2k-from-a2m \ MODELNAME=5csmA+1ecm.t2k joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: Nothing to be done for `joint'. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make -k PRED=1ecmA PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ecmA/xxxx-1ecmA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1sesA PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sesA/xxxx-1sesA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1auiA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1auiA/xxxx-1auiA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1bxnA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bxnA/struct-align/1bxnA.fssp-w0.5.mod', needed by `1bxnA/1bxnA-T0086-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t99-w0.5.mod', needed by `1bxnA/1bxnA-T0086-local.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxnA/xxxx-1bxnA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1burA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1burA/xxxx-1burA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1nal3 PRED2=1n joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nal3/xxxx-1nal3-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1pymA PRED2=1p joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pymA/xxxx-1pymA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1qu9A PRED2=1q joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qu9A/xxxx-1qu9A-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1cliA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cliA/xxxx-1cliA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1ctt PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctt/xxxx-1ctt-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1qf6A PRED2=1q joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qf6A/xxxx-1qf6A-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1atiA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1atiA/xxxx-1atiA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1adjA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1adjA/xxxx-1adjA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1pysA PRED2=1p joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pysA/xxxx-1pysA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1c0aA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c0aA/xxxx-1c0aA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=12asA PRED2=12 joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `12asA/xxxx-12asA-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1cg2A PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.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/1cg2A/struct-align/1cg2A.fssp.a2m.gz (14 sequences, 389 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054/tmp.a2m. Dropping 3 (of 14) duplicate sequences with differing IDs 11 sequences left after dropping 3 of 14 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054/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-4054/tmp.a2m (11 sequences, 389 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 1cg2A fixmode 1cg2A make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/1cg2A-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cg2A/struct-align/1cg2A.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-4054/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: -213.934036 Database has 3 sequences with 946 residues. gzip -f 1cg2A/1cg2A-T0086-fssp-global.pw.a2m make 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1cg2A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/T0086-1cg2A-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0086.t2k-w0.5.mod T0086.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0086.t2k.a2m.gz SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -77.965294 Database has 3 sequences with 946 residues. gzip -f 1cg2A/T0086-1cg2A-local.pw.a2m make 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1cg2A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/1cg2A-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9303/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -167.154617 Database has 3 sequences with 946 residues. gzip -f 1cg2A/1cg2A-T0086-local.pw.a2m make 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1cg2A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/T0086-1cg2A-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0086.t2k-w0.5.mod T0086.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0086.t2k.a2m.gz SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -72.521278 Database has 3 sequences with 946 residues. gzip -f 1cg2A/T0086-1cg2A-vit.pw.a2m make 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1cg2A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/1cg2A-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9303/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -161.982956 Database has 3 sequences with 946 residues. gzip -f 1cg2A/1cg2A-T0086-vit.pw.a2m make 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1cg2A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/T0086-1cg2A-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0086.t2k-w0.5.mod T0086.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0086.t2k.a2m.gz 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: -36.191723 Database has 3 sequences with 946 residues. gzip -f 1cg2A/T0086-1cg2A-global.pw.a2m make 1cg2A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1cg2A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1cg2A/1cg2A-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cg2A/info/1cg2A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cg2A/nostruct-align/1cg2A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9303/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: -154.510056 Database has 3 sequences with 946 residues. gzip -f 1cg2A/1cg2A-T0086-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cg2A/xxxx-1cg2A-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored) make -k PRED=1bouB PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.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/1bouB/struct-align/1bouB.fssp.a2m.gz (4 sequences, 298 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129/tmp.a2m. Dropping 3 (of 4) duplicate sequences with differing IDs 1 sequences left after dropping 3 of 4 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129/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-23129/tmp.a2m (1 sequences, 298 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 1bouB fixmode 1bouB make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/1bouB-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bouB/struct-align/1bouB.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-23129/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: -319.916351 Database has 3 sequences with 764 residues. gzip -f 1bouB/1bouB-T0086-fssp-global.pw.a2m make 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bouB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/T0086-1bouB-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0086.t2k-w0.5.mod T0086.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0086.t2k.a2m.gz SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -79.701241 Database has 3 sequences with 764 residues. gzip -f 1bouB/T0086-1bouB-local.pw.a2m make 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bouB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/1bouB-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13789/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -202.471603 Database has 3 sequences with 764 residues. gzip -f 1bouB/1bouB-T0086-local.pw.a2m make 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bouB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/T0086-1bouB-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0086.t2k-w0.5.mod T0086.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0086.t2k.a2m.gz SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -75.855225 Database has 3 sequences with 764 residues. gzip -f 1bouB/T0086-1bouB-vit.pw.a2m make 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bouB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/1bouB-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13789/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -199.221237 Database has 3 sequences with 764 residues. gzip -f 1bouB/1bouB-T0086-vit.pw.a2m make 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bouB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/T0086-1bouB-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0086.t2k-w0.5.mod T0086.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0086.t2k.a2m.gz 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: -52.223705 Database has 3 sequences with 764 residues. gzip -f 1bouB/T0086-1bouB-global.pw.a2m make 1bouB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bouB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bouB/1bouB-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bouB/info/1bouB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bouB/nostruct-align/1bouB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13789/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: -194.298691 Database has 3 sequences with 764 residues. gzip -f 1bouB/1bouB-T0086-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bouB/xxxx-1bouB-T0086-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' make: [joints] Error 2 (ignored)