make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/1nseA-T0098-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -347.389648 Database has 3 sequences with 981 residues. gzip -f 1nseA/1nseA-T0098-local.pw.a2m make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/1nseA-T0098-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -345.066650 Database has 3 sequences with 981 residues. gzip -f 1nseA/1nseA-T0098-vit.pw.a2m make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/1nseA-T0098-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nseA/nostruct-align/1nseA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-11/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -341.868683 Database has 3 sequences with 981 residues. gzip -f 1nseA/1nseA-T0098-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/1bxm-T0098-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22237/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -95.447021 Database has 3 sequences with 319 residues. gzip -f 1bxm/1bxm-T0098-local.pw.a2m make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/1bxm-T0098-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22237/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -92.716675 Database has 3 sequences with 319 residues. gzip -f 1bxm/1bxm-T0098-vit.pw.a2m make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/1bxm-T0098-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1bxm/nostruct-align/1bxm.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22237/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -98.851341 Database has 3 sequences with 319 residues. gzip -f 1bxm/1bxm-T0098-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/1au7A-T0098-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9876/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -51.733051 Database has 3 sequences with 397 residues. gzip -f 1au7A/1au7A-T0098-local.pw.a2m make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/1au7A-T0098-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9876/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.969707 Database has 3 sequences with 397 residues. gzip -f 1au7A/1au7A-T0098-vit.pw.a2m make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/1au7A-T0098-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod -db T0098.seq -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1au7A/nostruct-align/1au7A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9876/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -45.780018 Database has 3 sequences with 397 residues. gzip -f 1au7A/1au7A-T0098-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0098.t2k.2d.rdb T0098.t2k-2d.mod make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/T0098-1nseA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1nseA Error in locating FIM delete in 1nseA . Average NLL-Simple NULL score: -42.333946 Database has 3 sequences with 981 residues. gzip -f 1nseA/T0098-1nseA-2track-local.pw.a2m make[1]: *** No rule to make target ` ', needed by `joint'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/T0098-1bxm-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1bxm Error in locating FIM delete in 1bxm . Average NLL-Simple NULL score: -43.304493 Database has 3 sequences with 319 residues. gzip -f 1bxm/T0098-1bxm-2track-local.pw.a2m make[1]: *** No rule to make target ` ', needed by `joint'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/T0098-1au7A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1au7A Error in locating FIM delete in 1au7A . Average NLL-Simple NULL score: -40.387035 Database has 3 sequences with 397 residues. gzip -f 1au7A/T0098-1au7A-2track-local.pw.a2m make[1]: *** No rule to make target ` ', needed by `joint'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/T0098-1nseA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1nseA Error in locating FIM delete in 1nseA . Average NLL-Simple NULL score: -42.333946 Database has 3 sequences with 981 residues. gzip -f 1nseA/T0098-1nseA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/T0098-1bxm-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1bxm Error in locating FIM delete in 1bxm . Average NLL-Simple NULL score: -43.304493 Database has 3 sequences with 319 residues. gzip -f 1bxm/T0098-1bxm-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/T0098-1au7A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1au7A Error in locating FIM delete in 1au7A . Average NLL-Simple NULL score: -40.387035 Database has 3 sequences with 397 residues. gzip -f 1au7A/T0098-1au7A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/T0098-1nseA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.333946 Database has 3 sequences with 981 residues. gzip -f 1nseA/T0098-1nseA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/T0098-1bxm-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.304493 Database has 3 sequences with 319 residues. gzip -f 1bxm/T0098-1bxm-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/T0098-1au7A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.387035 Database has 3 sequences with 397 residues. gzip -f 1au7A/T0098-1au7A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/T0098-1nseA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.333946 Database has 3 sequences with 981 residues. gzip -f 1nseA/T0098-1nseA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/T0098-1bxm-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.304493 Database has 3 sequences with 319 residues. gzip -f 1bxm/T0098-1bxm-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/T0098-1au7A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -40.387035 Database has 3 sequences with 397 residues. gzip -f 1au7A/T0098-1au7A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1nseA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1nseA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1nseA/T0098-1nseA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nseA/info/1nseA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 7745.611816 Database has 3 sequences with 981 residues. gzip -f 1nseA/T0098-1nseA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1bxm make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1bxm' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1bxm/T0098-1bxm-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bxm/info/1bxm.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -30.112671 Database has 3 sequences with 319 residues. gzip -f 1bxm/T0098-1bxm-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make 1au7A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[2]: `1au7A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' hmmscore 1au7A/T0098-1au7A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0098.t2k-w0.5.mod,T0098.t2k-2d.mod \ -db T0098.seq,T0098.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1au7A/info/1au7A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0098.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9049/tmp.a2m T0098.t2k-2d.mod(749): Reading track 1 model from MODEL -- Model from 2nd structure file T0098.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 252.327148 Database has 3 sequences with 397 residues. gzip -f 1au7A/T0098-1au7A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1nseA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nseA/xxxx-1nseA-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1bxm PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bxm/xxxx-1bxm-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1au7A PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1au7A/xxxx-1au7A-T0098-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t98' make: [joints] Error 2 (ignored) make -k PRED=1di2A PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t98' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1di2A/struct-align/1di2A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1di2A/struct-align/1di2A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20574 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20574/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1d/1di2A/struct-align/1di2A.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1d/1di2A/struct-align/1di2A.fssp.a2m.gz (4 sequences, 69 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20574/tmp.a2m. Dropping 1 (of 4) sequences with > 80.0% id 3 sequences left after dropping 1 of 4 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20574/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20574/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20574/tmp.a2m (3 sequences, 69 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20574/tmp.mod /projects/compbio/experiments/models.97/pdb/1d/1di2A/struct-align/1di2A.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20574 80.0% id 48 sequences left after dropping 22 of 70 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16988/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16988/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16988/tmp.a2m (48 sequences, 339 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16988/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qpzA/struct-align/1qpzA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16988 80.0% id 1 sequences left after dropping 1 of 2 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17163/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17163/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17163/tmp.a2m (1 sequences, 93 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17163/tmp.mod /projects/compbio/experiments/models.97/pdb/2e/2ezk/struct-align/2ezk.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17163