make -k PRED=1xvaA PRED2=1x joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp.a2m.gz (28 sequences, 293 columns) as A2M alignment. make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' mkdir 1xvaA fixmode 1xvaA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp.a2m.gz 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: -290.855530 Database has 2 sequences with 534 residues. gzip -f 1xvaA/1xvaA-T0092-fssp-global.pw.a2m /projects/compbio/experiments/models.97/scripts/w0.5 T0092.t2k.a2m.gz T0092.t2k-w0.5.mod 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 T0092.t2k.a2m.gz (131 sequences, 241 columns) as A2M alignment. make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/T0092-1xvaA-local.pw -i T0092.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0092.t2k-w0.5.mod T0092.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0092.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -120.232025 Database has 2 sequences with 534 residues. gzip -f 1xvaA/T0092-1xvaA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod', needed by `1xvaA/1xvaA-T0092-local.pw.a2m.gz'. make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/T0092-1xvaA-vit.pw \ -i T0092.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0092.t2k-w0.5.mod T0092.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0092.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -115.055511 Database has 2 sequences with 534 residues. gzip -f 1xvaA/T0092-1xvaA-vit.pw.a2m make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/T0092-1xvaA-global.pw -i T0092.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0092.t2k-w0.5.mod T0092.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0092.t2k.a2m.gz 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: -218.957550 Database has 2 sequences with 534 residues. gzip -f 1xvaA/T0092-1xvaA-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1xvaA/xxxx-1xvaA-T0092-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' make: [joints] Error 2 (ignored) make -k PRED=1xvaA PRED2=1x joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz (254 sequences, 293 columns) as A2M alignment. make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-local.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -165.832550 Database has 2 sequences with 534 residues. gzip -f 1xvaA/1xvaA-T0092-local.pw.a2m make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -159.689575 Database has 2 sequences with 534 residues. gzip -f 1xvaA/1xvaA-T0092-vit.pw.a2m make 1xvaA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-global.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz 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: -269.183044 Database has 2 sequences with 534 residues. gzip -f 1xvaA/1xvaA-T0092-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1xvaA/xxxx-1xvaA-T0092-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t92' make: [joints] Error 2 (ignored) make -k PRED=1xvaA PRED2=1x joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/struct-align/1xvaA.fssp.a2m.gz 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: -364.536377 Database has 3 sequences with 827 residues. gzip -f 1xvaA/1xvaA-T0092-fssp-global.pw.a2m make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/T0092-1xvaA-local.pw -i T0092.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0092.t2k-w0.5.mod T0092.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0092.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -97.654625 Database has 3 sequences with 827 residues. gzip -f 1xvaA/T0092-1xvaA-local.pw.a2m make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-local.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -204.537659 Database has 3 sequences with 827 residues. gzip -f 1xvaA/1xvaA-T0092-local.pw.a2m make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/T0092-1xvaA-vit.pw \ -i T0092.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0092.t2k-w0.5.mod T0092.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0092.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -91.161621 Database has 3 sequences with 827 residues. gzip -f 1xvaA/T0092-1xvaA-vit.pw.a2m make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -199.836685 Database has 3 sequences with 827 residues. gzip -f 1xvaA/1xvaA-T0092-vit.pw.a2m make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/T0092-1xvaA-global.pw -i T0092.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0092.t2k-w0.5.mod T0092.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0092.t2k.a2m.gz 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: -194.811386 Database has 3 sequences with 827 residues. gzip -f 1xvaA/T0092-1xvaA-global.pw.a2m make 1xvaA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t92' make[2]: `1xvaA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' hmmscore 1xvaA/1xvaA-T0092-global.pw -i /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod -db T0092.seq -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1x/1xvaA/info/1xvaA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1x/1xvaA/nostruct-align/1xvaA.t2k.a2m.gz 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: -313.967377 Database has 3 sequences with 827 residues. gzip -f 1xvaA/1xvaA-T0092-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1xvaA/xxxx-1xvaA-T0092-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t92' make: [joints] Error 2 (ignored)