echo remote 2track remote 2track make -k PRED=1cr6B PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make -k \ 1cr6B/T0120-211-end-1cr6B-local.pw.a2m.gz 1cr6B/1cr6B-T0120-211-end-local.pw.a2m.gz \ 1cr6B/T0120-211-end-1cr6B-2track-local.pw.a2m.gz \ 1cr6B/T0120-211-end-1cr6B-2track-global.pw.a2m.gz \ 1cr6B/T0120-211-end-1cr6B-vit.pw.a2m.gz 1cr6B/1cr6B-T0120-211-end-vit.pw.a2m.gz \ 1cr6B/T0120-211-end-1cr6B-global.pw.a2m.gz 1cr6B/1cr6B-T0120-211-end-global.pw.a2m.gz \ 1cr6B/1cr6B-T0120-211-end-fssp-global.pw.a2m.gz \ 1cr6B/xxxx-1cr6B-T0120-211-end-local.pw.a2m.gz 1cr6B/xxxx-1cr6B-T0120-211-end-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' mkdir 1cr6B fixmode 1cr6B make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0120-211-end-1cr6B-local.pw -i T0120-211-end.remote-t2k-w0.5.mod -db T0120-211-end.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-211-end.remote-t2k-w0.5.mod T0120-211-end.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.055378 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/T0120-211-end-1cr6B-local.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0120-211-end-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod -db T0120-211-end.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16293/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -274.004364 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/1cr6B-T0120-211-end-local.pw.a2m /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0120-211-end.remote-t2k.2d.rdb T0120-211-end.remote-t2k-2d.mod make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0120-211-end-1cr6B-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-211-end.remote-t2k-w0.5.mod,T0120-211-end.remote-t2k-2d.mod \ -db T0120-211-end.seq,T0120-211-end.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 T0120-211-end.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.a2m T0120-211-end.remote-t2k-2d.mod(785): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-211-end.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.498535 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/T0120-211-end-1cr6B-2track-local.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0120-211-end-1cr6B-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-211-end.remote-t2k-w0.5.mod,T0120-211-end.remote-t2k-2d.mod \ -db T0120-211-end.seq,T0120-211-end.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0120-211-end.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.a2m T0120-211-end.remote-t2k-2d.mod(785): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-211-end.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 31.011175 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/T0120-211-end-1cr6B-2track-global.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0120-211-end-1cr6B-vit.pw \ -i T0120-211-end.remote-t2k-w0.5.mod -db T0120-211-end.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-211-end.remote-t2k-w0.5.mod T0120-211-end.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.837708 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/T0120-211-end-1cr6B-vit.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0120-211-end-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod -db T0120-211-end.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16293/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -270.264374 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/1cr6B-T0120-211-end-vit.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/T0120-211-end-1cr6B-global.pw -i T0120-211-end.remote-t2k-w0.5.mod -db T0120-211-end.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-211-end.remote-t2k-w0.5.mod T0120-211-end.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 18.141663 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/T0120-211-end-1cr6B-global.pw.a2m make 1cr6B make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' make[3]: `1cr6B' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-211-end' /projects/compbio/bin/alpha.new/hmmscore 1cr6B/1cr6B-T0120-211-end-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod -db T0120-211-end.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cr6B/info/1cr6B.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/nostruct-align/1cr6B.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16293/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -267.084991 Database has 3 sequences with 1221 residues. gzip -f 1cr6B/1cr6B-T0120-211-end-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6018 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6018/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.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/1c/1cr6B/struct-align/1cr6B.fssp.a2m.gz (31 sequences, 541 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6018/tmp.a2m. Dropping 2 (of 31) duplicate sequences with differing IDs Dropping 1 (of 31) sequences with > 80.0% id 28 sequences left after dropping 3 of 31 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6018/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6018/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-6018/tmp.a2m (28 sequences, 541 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6018/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cr6B/struct-align/1cr6B.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6018 80.0% id 3 sequences left after dropping 49 of 52 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5840/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5840/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-5840/tmp.a2m (3 sequences, 221 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5840/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a8rA/struct-align/1a8rA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5840