make -k PRED=1sesA PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz', needed by `/projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod'. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 1sesA fixmode 1sesA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-const-global.pw -i -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -viterbi 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Error: Couldn't open file -db: No such file or directory make[1]: *** [1sesA/1sesA-T0086-const-global.pw.a2m.gz] Error 1 /projects/compbio/experiments/models.97/scripts/w0.5 T0086.t2k.a2m.gz T0086.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 T0086.t2k.a2m.gz (6 sequences, 164 columns) as A2M alignment. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -110.281799 Database has 2 sequences with 585 residues. gzip -f 1sesA/T0086-1sesA-vit.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz', needed by `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod'. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -viterbi 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 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: -205.816528 Database has 2 sequences with 585 residues. gzip -f 1sesA/T0086-1sesA-global.pw.a2m 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 `/projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz', needed by `/projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod'. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -115.701805 Database has 2 sequences with 585 residues. gzip -f 1sesA/T0086-1sesA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/1sesA-T0086-local.pw.a2m.gz'. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 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: -205.816528 Database has 2 sequences with 585 residues. gzip -f 1sesA/T0086-1sesA-global.pw.a2m 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 `/projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz', needed by `/projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod'. make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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=1sesA PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.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/1s/1sesA/struct-align/1sesA.fssp.a2m.gz (29 sequences, 421 columns) as A2M alignment. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 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: -289.235046 Database has 2 sequences with 585 residues. gzip -f 1sesA/1sesA-T0086-fssp-global.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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=1sesA PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.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/1a/1auiA/struct-align/1auiA.fssp.a2m.gz (5 sequences, 378 columns) as A2M alignment. make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 1auiA fixmode 1auiA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 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: -279.689056 Database has 2 sequences with 685 residues. gzip -f 1auiA/1auiA-T0086-fssp-global.pw.a2m make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/T0086-1auiA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -117.871727 Database has 2 sequences with 685 residues. gzip -f 1auiA/T0086-1auiA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod', needed by `1auiA/1auiA-T0086-local.pw.a2m.gz'. make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/T0086-1auiA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -112.966736 Database has 2 sequences with 685 residues. gzip -f 1auiA/T0086-1auiA-vit.pw.a2m make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/T0086-1auiA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 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: -218.095581 Database has 2 sequences with 685 residues. gzip -f 1auiA/T0086-1auiA-global.pw.a2m 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 1bxnA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 1bxnA fixmode 1bxnA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/T0086-1bxnA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -116.644554 Database has 2 sequences with 650 residues. gzip -f 1bxnA/T0086-1bxnA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod', needed by `1bxnA/1bxnA-T0086-local.pw.a2m.gz'. make 1bxnA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/T0086-1bxnA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -112.448547 Database has 2 sequences with 650 residues. gzip -f 1bxnA/T0086-1bxnA-vit.pw.a2m make 1bxnA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/T0086-1bxnA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:03 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: -209.327087 Database has 2 sequences with 650 residues. gzip -f 1bxnA/T0086-1bxnA-global.pw.a2m 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=2chsA PRED2=2c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.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/2c/2chsA/struct-align/2chsA.fssp.a2m.gz (36 sequences, 114 columns) as A2M alignment. make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 2chsA fixmode 2chsA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.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: -139.090012 Database has 2 sequences with 291 residues. gzip -f 2chsA/2chsA-T0086-fssp-global.pw.a2m make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/T0086-2chsA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -113.852013 Database has 2 sequences with 291 residues. gzip -f 2chsA/T0086-2chsA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod', needed by `2chsA/2chsA-T0086-local.pw.a2m.gz'. make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/T0086-2chsA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -110.051010 Database has 2 sequences with 291 residues. gzip -f 2chsA/T0086-2chsA-vit.pw.a2m make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/T0086-2chsA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.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 v3.1b (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: -167.840500 Database has 2 sequences with 291 residues. gzip -f 2chsA/T0086-2chsA-global.pw.a2m 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 `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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 `/projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod', needed by `1auiA/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.t2k-w0.5.mod', needed by `1bxnA/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=2chsA PRED2=2c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod', needed by `2chsA/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 joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.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/5c/5csmA/struct-align/5csmA.fssp.a2m.gz (9 sequences, 250 columns) as A2M alignment. make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 5csmA fixmode 5csmA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.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: -287.296021 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA-T0086-fssp-global.pw.a2m make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/T0086-5csmA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -115.362022 Database has 2 sequences with 420 residues. gzip -f 5csmA/T0086-5csmA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod', needed by `5csmA/5csmA-T0086-local.pw.a2m.gz'. make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/T0086-5csmA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -111.347046 Database has 2 sequences with 420 residues. gzip -f 5csmA/T0086-5csmA-vit.pw.a2m make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/T0086-5csmA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.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 v3.1b (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: -188.181519 Database has 2 sequences with 420 residues. gzip -f 5csmA/T0086-5csmA-global.pw.a2m 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 `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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 `/projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod', needed by `1auiA/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.t2k-w0.5.mod', needed by `1bxnA/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=2chsA PRED2=2c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod', needed by `2chsA/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 joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod', needed by `5csmA/5csmA-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 `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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 `/projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod', needed by `1auiA/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.t2k-w0.5.mod', needed by `1bxnA/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=2chsA PRED2=2c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod', needed by `2chsA/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 joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod', needed by `5csmA/5csmA-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=1ecmA PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.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/1e/1ecmA/struct-align/1ecmA.fssp.a2m.gz (19 sequences, 91 columns) as A2M alignment. make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' mkdir 1ecmA fixmode 1ecmA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.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: -43.839020 Database has 2 sequences with 273 residues. gzip -f 1ecmA/1ecmA-T0086-fssp-global.pw.a2m make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/T0086-1ecmA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -114.733910 Database has 2 sequences with 273 residues. gzip -f 1ecmA/T0086-1ecmA-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod', needed by `1ecmA/1ecmA-T0086-local.pw.a2m.gz'. make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/T0086-1ecmA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -110.873413 Database has 2 sequences with 273 residues. gzip -f 1ecmA/T0086-1ecmA-vit.pw.a2m make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/T0086-1ecmA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.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 v3.1b (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: -166.508499 Database has 2 sequences with 273 residues. gzip -f 1ecmA/T0086-1ecmA-global.pw.a2m 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 `/projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod', needed by `1sesA/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 `/projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod', needed by `1auiA/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.t2k-w0.5.mod', needed by `1bxnA/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=2chsA PRED2=2c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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/2c/2chsA/nostruct-align/2chsA.t2k.a2m.gz (6 sequences, 114 columns) as A2M alignment. make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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: -81.296997 Database has 2 sequences with 291 residues. gzip -f 2chsA/2chsA-T0086-local.pw.a2m make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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: -77.904503 Database has 2 sequences with 291 residues. gzip -f 2chsA/2chsA-T0086-vit.pw.a2m make 2chsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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: -135.674530 Database has 2 sequences with 291 residues. gzip -f 2chsA/2chsA-T0086-global.pw.a2m 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 joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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/5c/5csmA/nostruct-align/5csmA.t2k.a2m.gz (17 sequences, 250 columns) as A2M alignment. make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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: -159.952026 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA-T0086-local.pw.a2m make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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: -156.068024 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA-T0086-vit.pw.a2m make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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: -241.671539 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA-T0086-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5csmA/xxxx-5csmA-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=1ecmA PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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/1e/1ecmA/nostruct-align/1ecmA.t2k.a2m.gz (35 sequences, 91 columns) as A2M alignment. make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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: -50.697411 Database has 2 sequences with 273 residues. gzip -f 1ecmA/1ecmA-T0086-local.pw.a2m make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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: -47.939919 Database has 2 sequences with 273 residues. gzip -f 1ecmA/1ecmA-T0086-vit.pw.a2m make 1ecmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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: -88.194527 Database has 2 sequences with 273 residues. gzip -f 1ecmA/1ecmA-T0086-global.pw.a2m 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' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz (122 sequences, 421 columns) as A2M alignment. make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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: -190.068329 Database has 2 sequences with 585 residues. gzip -f 1sesA/1sesA-T0086-local.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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: -184.027847 Database has 2 sequences with 585 residues. gzip -f 1sesA/1sesA-T0086-vit.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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: -293.576538 Database has 2 sequences with 585 residues. gzip -f 1sesA/1sesA-T0086-global.pw.a2m 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 `/projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod', needed by `1auiA/1auiA-T0086-local.pw.a2m.gz'. 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.t2k-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=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' gzip -f 5csmA/5csmA+1ecm.a2m /projects/compbio/experiments/models.97/scripts/w0.5 5csmA/5csmA+1ecm.a2m.gz 5csmA/5csmA+1ecm-w0.5.mod Sequence 1ecmAB has 251 alignment columns, but previously alignment width set to 250 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 File 5csmA/5csmA+1ecm.a2m.gz (2 sequences) does not look like an alignment. There must be the same number of columns in each sequence. In a2m format, a column is a capital letter or -. If each sequence does not have the same number of capitals and hyphens, SAM will try treating every uppercase, lowercase, period and hyphen as a column. SAM will ignore the alignment file. On the WWW server, SAM will train a model on the unaligned sequences. No alignment found in alignment file 5csmA/5csmA+1ecm.a2m.gz. Error: No alignment found from which to create a model. modelfromalign 5csmA/5csmA+1ecm.a2m.gz failed at /projects/compbio/experiments/models.97/scripts/build-weighted-model.pl line 70. Error: building weighted model 5csmA/5csmA+1ecm-w0.5.mod failed make[1]: *** [5csmA/5csmA+1ecm-w0.5.mod] Error 1 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=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' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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/1a/1auiA/nostruct-align/1auiA.t2k.a2m.gz (350 sequences, 378 columns) as A2M alignment. make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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: -203.754745 Database has 2 sequences with 685 residues. gzip -f 1auiA/1auiA-T0086-local.pw.a2m make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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: -199.457230 Database has 2 sequences with 685 residues. gzip -f 1auiA/1auiA-T0086-vit.pw.a2m make 1auiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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: -309.938599 Database has 2 sequences with 685 residues. gzip -f 1auiA/1auiA-T0086-global.pw.a2m 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.t2k-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=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' gzip -f 5csmA/5csmA+1ecm.a2m /projects/compbio/experiments/models.97/scripts/w0.5 5csmA/5csmA+1ecm.a2m.gz 5csmA/5csmA+1ecm-w0.5.mod Sequence 1ecmAB has 249 alignment columns, but previously alignment width set to 250 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 File 5csmA/5csmA+1ecm.a2m.gz (2 sequences) does not look like an alignment. There must be the same number of columns in each sequence. In a2m format, a column is a capital letter or -. If each sequence does not have the same number of capitals and hyphens, SAM will try treating every uppercase, lowercase, period and hyphen as a column. SAM will ignore the alignment file. On the WWW server, SAM will train a model on the unaligned sequences. No alignment found in alignment file 5csmA/5csmA+1ecm.a2m.gz. Error: No alignment found from which to create a model. modelfromalign 5csmA/5csmA+1ecm.a2m.gz failed at /projects/compbio/experiments/models.97/scripts/build-weighted-model.pl line 70. Error: building weighted model 5csmA/5csmA+1ecm-w0.5.mod failed make[1]: *** [5csmA/5csmA+1ecm-w0.5.mod] Error 1 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=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.t2k-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=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' /projects/compbio/experiments/models.97/scripts/w0.5 5csmA/5csmA+1ecm.a2m.gz 5csmA/5csmA+1ecm-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 5csmA/5csmA+1ecm.a2m.gz (2 sequences, 250 columns) as A2M alignment. make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm-5csmA-T0086-local.pw -i 5csmA/5csmA+1ecm-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm-w0.5.mod 5csmA/5csmA+1ecm-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.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: -178.970520 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA+1ecm-5csmA-T0086-local.pw.a2m make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm-5csmA-T0086-global.pw -i 5csmA/5csmA+1ecm-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm-w0.5.mod 5csmA/5csmA+1ecm-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.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: -304.979553 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA+1ecm-5csmA-T0086-global.pw.a2m 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.t2k-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=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' /projects/compbio/experiments/models.97/scripts/w0.5 5csmA/5csmA+1ecm.t2k-from-a2m.a2m.gz 5csmA/5csmA+1ecm.t2k-from-a2m-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 5csmA/5csmA+1ecm.t2k-from-a2m.a2m.gz (41 sequences, 250 columns) as A2M alignment. make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm.t2k-5csmA-T0086-local.pw -i 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.t2k-from-a2m.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: -147.589539 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA+1ecm.t2k-5csmA-T0086-local.pw.a2m make 5csmA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm.t2k-5csmA-T0086-global.pw -i 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.t2k-from-a2m.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: -235.059540 Database has 2 sequences with 420 residues. gzip -f 5csmA/5csmA+1ecm.t2k-5csmA-T0086-global.pw.a2m 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'. /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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/1b/1bxnA/nostruct-align/1bxnA.t2k.a2m.gz (4561 sequences, 445 columns) as A2M alignment. make 1bxnA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/1bxnA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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: -251.672012 Database has 2 sequences with 650 residues. gzip -f 1bxnA/1bxnA-T0086-local.pw.a2m make 1bxnA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/1bxnA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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: -248.305527 Database has 2 sequences with 650 residues. gzip -f 1bxnA/1bxnA-T0086-vit.pw.a2m make 1bxnA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/1bxnA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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: -360.202087 Database has 2 sequences with 650 residues. gzip -f 1bxnA/1bxnA-T0086-global.pw.a2m 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=2chsA PRED2=2c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/struct-align/2chsA.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: -169.526352 Database has 3 sequences with 405 residues. gzip -f 2chsA/2chsA-T0086-fssp-global.pw.a2m make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/T0086-2chsA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -79.029617 Database has 3 sequences with 405 residues. gzip -f 2chsA/T0086-2chsA-local.pw.a2m make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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: -105.507607 Database has 3 sequences with 405 residues. gzip -f 2chsA/2chsA-T0086-local.pw.a2m make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/T0086-2chsA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -74.496948 Database has 3 sequences with 405 residues. gzip -f 2chsA/T0086-2chsA-vit.pw.a2m make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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: -102.869270 Database has 3 sequences with 405 residues. gzip -f 2chsA/2chsA-T0086-vit.pw.a2m make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/T0086-2chsA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.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 v3.1b (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: -124.917999 Database has 3 sequences with 405 residues. gzip -f 2chsA/T0086-2chsA-global.pw.a2m make 2chsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `2chsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 2chsA/2chsA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2c/2chsA/info/2chsA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/2c/2chsA/nostruct-align/2chsA.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: -161.240036 Database has 3 sequences with 405 residues. gzip -f 2chsA/2chsA-T0086-global.pw.a2m 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 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/struct-align/5csmA.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: -359.793701 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA-T0086-fssp-global.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/T0086-5csmA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -81.079872 Database has 3 sequences with 670 residues. gzip -f 5csmA/T0086-5csmA-local.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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: -210.414871 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA-T0086-local.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/T0086-5csmA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -76.196877 Database has 3 sequences with 670 residues. gzip -f 5csmA/T0086-5csmA-vit.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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: -207.375854 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA-T0086-vit.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/T0086-5csmA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.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 v3.1b (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: -153.125015 Database has 3 sequences with 670 residues. gzip -f 5csmA/T0086-5csmA-global.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/5c/5csmA/nostruct-align/5csmA.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: -301.454041 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA-T0086-global.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm-5csmA-T0086-local.pw -i 5csmA/5csmA+1ecm-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm-w0.5.mod 5csmA/5csmA+1ecm-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.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: -236.062195 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA+1ecm-5csmA-T0086-local.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm-5csmA-T0086-global.pw -i 5csmA/5csmA+1ecm-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm-w0.5.mod 5csmA/5csmA+1ecm-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.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: -373.658691 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA+1ecm-5csmA-T0086-global.pw.a2m 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 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm.t2k-5csmA-T0086-local.pw -i 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.t2k-from-a2m.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: -193.955551 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA+1ecm.t2k-5csmA-T0086-local.pw.a2m make 5csmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `5csmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 5csmA/5csmA+1ecm.t2k-5csmA-T0086-global.pw -i 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5c/5csmA/info/5csmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod 5csmA/5csmA+1ecm.t2k-from-a2m-w0.5.mod(23): Reading MODEL -- Model from alignment file 5csmA/5csmA+1ecm.t2k-from-a2m.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: -290.876038 Database has 3 sequences with 670 residues. gzip -f 5csmA/5csmA+1ecm.t2k-5csmA-T0086-global.pw.a2m 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 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/struct-align/1ecmA.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: -62.085682 Database has 3 sequences with 364 residues. gzip -f 1ecmA/1ecmA-T0086-fssp-global.pw.a2m make 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/T0086-1ecmA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -80.180321 Database has 3 sequences with 364 residues. gzip -f 1ecmA/T0086-1ecmA-local.pw.a2m make 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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: -64.129326 Database has 3 sequences with 364 residues. gzip -f 1ecmA/1ecmA-T0086-local.pw.a2m make 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/T0086-1ecmA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -75.617661 Database has 3 sequences with 364 residues. gzip -f 1ecmA/T0086-1ecmA-vit.pw.a2m make 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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: -61.785328 Database has 3 sequences with 364 residues. gzip -f 1ecmA/1ecmA-T0086-vit.pw.a2m make 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/T0086-1ecmA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.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 v3.1b (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: -121.726677 Database has 3 sequences with 364 residues. gzip -f 1ecmA/T0086-1ecmA-global.pw.a2m make 1ecmA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1ecmA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1ecmA/1ecmA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1ecmA/info/1ecmA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1e/1ecmA/nostruct-align/1ecmA.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: -102.420692 Database has 3 sequences with 364 residues. gzip -f 1ecmA/1ecmA-T0086-global.pw.a2m 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 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.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: -388.597412 Database has 3 sequences with 1006 residues. gzip -f 1sesA/1sesA-T0086-fssp-global.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -81.527687 Database has 3 sequences with 1006 residues. gzip -f 1sesA/T0086-1sesA-local.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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: -246.723709 Database has 3 sequences with 1006 residues. gzip -f 1sesA/1sesA-T0086-local.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -74.768677 Database has 3 sequences with 1006 residues. gzip -f 1sesA/T0086-1sesA-vit.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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: -242.232742 Database has 3 sequences with 1006 residues. gzip -f 1sesA/1sesA-T0086-vit.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/T0086-1sesA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.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 v3.1b (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: -177.446365 Database has 3 sequences with 1006 residues. gzip -f 1sesA/T0086-1sesA-global.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1sesA/1sesA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.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: -376.257050 Database has 3 sequences with 1006 residues. gzip -f 1sesA/1sesA-T0086-global.pw.a2m 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 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/struct-align/1auiA.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: -376.823090 Database has 3 sequences with 1063 residues. gzip -f 1auiA/1auiA-T0086-fssp-global.pw.a2m make 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/T0086-1auiA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -84.480202 Database has 3 sequences with 1063 residues. gzip -f 1auiA/T0086-1auiA-local.pw.a2m make 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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: -266.866852 Database has 3 sequences with 1063 residues. gzip -f 1auiA/1auiA-T0086-local.pw.a2m make 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/T0086-1auiA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -78.455528 Database has 3 sequences with 1063 residues. gzip -f 1auiA/T0086-1auiA-vit.pw.a2m make 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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: -262.988159 Database has 3 sequences with 1063 residues. gzip -f 1auiA/1auiA-T0086-vit.pw.a2m make 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/T0086-1auiA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.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 v3.1b (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: -183.429077 Database has 3 sequences with 1063 residues. gzip -f 1auiA/T0086-1auiA-global.pw.a2m make 1auiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1auiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1auiA/1auiA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1auiA/info/1auiA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1a/1auiA/nostruct-align/1auiA.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: -389.725433 Database has 3 sequences with 1063 residues. gzip -f 1auiA/1auiA-T0086-global.pw.a2m 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 1bxnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/T0086-1bxnA-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -82.813698 Database has 3 sequences with 1095 residues. gzip -f 1bxnA/T0086-1bxnA-local.pw.a2m make 1bxnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/1bxnA-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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: -331.756012 Database has 3 sequences with 1095 residues. gzip -f 1bxnA/1bxnA-T0086-local.pw.a2m make 1bxnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/T0086-1bxnA-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.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 v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -77.687012 Database has 3 sequences with 1095 residues. gzip -f 1bxnA/T0086-1bxnA-vit.pw.a2m make 1bxnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/1bxnA-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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: -329.083008 Database has 3 sequences with 1095 residues. gzip -f 1bxnA/1bxnA-T0086-vit.pw.a2m make 1bxnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/T0086-1bxnA-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.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 v3.1b (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: -180.451096 Database has 3 sequences with 1095 residues. gzip -f 1bxnA/T0086-1bxnA-global.pw.a2m make 1bxnA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[2]: `1bxnA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1bxnA/1bxnA-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxnA/info/1bxnA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1b/1bxnA/nostruct-align/1bxnA.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: -468.604736 Database has 3 sequences with 1095 residues. gzip -f 1bxnA/1bxnA-T0086-global.pw.a2m 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)