echo remote 2track remote 2track make -k PRED=1svy PRED2=1s A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1svy/T0120-1-115-1svy-local.pw.a2m.gz 1svy/1svy-T0120-1-115-local.pw.a2m.gz \ 1svy/T0120-1-115-1svy-2track-local.pw.a2m.gz \ 1svy/T0120-1-115-1svy-2track-global.pw.a2m.gz \ 1svy/T0120-1-115-1svy-vit.pw.a2m.gz 1svy/1svy-T0120-1-115-vit.pw.a2m.gz \ 1svy/T0120-1-115-1svy-global.pw.a2m.gz 1svy/1svy-T0120-1-115-global.pw.a2m.gz \ 1svy/1svy-T0120-1-115-fssp-global.pw.a2m.gz \ 1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz 1svy/xxxx-1svy-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1svy/T0120-1-115-1svy-local.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-local.pw.a2m.gz' is up to date. echo ReadNeuralNet /projects/compbio/usr/karplus/predict-2nd/testing/networks/overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net > tmp.script echo ReadA2M T0120-1-115.remote-t2k.a2m.gz >> tmp.script echo PrintPrediction T0120-1-115.remote-t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0120-1-115.remote-t2k.2d.seq >> tmp.script echo PrintRDB T0120-1-115.remote-t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net # command:# Reading A2M format from T0120-1-115.remote-t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0120-1-115.remote-t2k.a2m with 5 sequences, total weight= 1.96701 avg weight= 0.393402 6 iterations Regularizing alignment for T0120-1-115.remote-t2k.a2m.gz # After reading T0120-1-115.remote-t2k.a2m.gz, have 115 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0120-1-115.remote-t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0120-1-115.remote-t2k.2d.seq # command:# Network initialization done # Printing prediction to T0120-1-115.remote-t2k.2d.rdb # command:rm tmp.script /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0120-1-115.remote-t2k.2d.rdb T0120-1-115.remote-t2k-2d.mod make 1svy make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1svy' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1svy/T0120-1-115-1svy-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.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 T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.798801 Database has 3 sequences with 331 residues. gzip -f 1svy/T0120-1-115-1svy-2track-local.pw.a2m make 1svy make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1svy' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1svy/T0120-1-115-1svy-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.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. T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -50.599171 Database has 3 sequences with 331 residues. gzip -f 1svy/T0120-1-115-1svy-2track-global.pw.a2m make 1svy make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1svy' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1svy/T0120-1-115-1svy-vit.pw \ -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -62.649639 Database has 3 sequences with 331 residues. gzip -f 1svy/T0120-1-115-1svy-vit.pw.a2m make 1svy make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1svy' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1svy/1svy-T0120-1-115-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1s/1svy/nostruct-align/1svy.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1svy/nostruct-align/1svy.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1svy/nostruct-align/1svy.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28384/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: -48.398640 Database has 3 sequences with 331 residues. gzip -f 1svy/1svy-T0120-1-115-vit.pw.a2m make 1svy make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1svy' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1svy/T0120-1-115-1svy-global.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -56.809998 Database has 3 sequences with 331 residues. gzip -f 1svy/T0120-1-115-1svy-global.pw.a2m make 1svy make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1svy' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1svy/1svy-T0120-1-115-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1svy/nostruct-align/1svy.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1svy/info/1svy.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1svy/nostruct-align/1svy.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1svy/nostruct-align/1svy.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28384/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: -48.389660 Database has 3 sequences with 331 residues. gzip -f 1svy/1svy-T0120-1-115-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1s/1svy/struct-align/1svy.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1s/1svy/struct-align/1svy.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7161 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7161/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1s/1svy/struct-align/1svy.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/1s/1svy/struct-align/1svy.fssp.a2m.gz (5 sequences, 102 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7161/tmp.a2m. Dropping 1 (of 5) duplicate sequences with differing IDs Dropping 1 (of 5) sequences with > 80.0% id 3 sequences left after dropping 2 of 5 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7161/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7161/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-7161/tmp.a2m (3 sequences, 102 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7161/tmp.mod /projects/compbio/experiments/models.97/pdb/1s/1svy/struct-align/1svy.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7161 80.0% id 1 sequences left after dropping 7 of 8 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15919/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15919/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-15919/tmp.a2m (1 sequences, 66 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15919/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1azpA/struct-align/1azpA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15919 80.0% id 3 sequences left after dropping 8 of 11 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14144/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14144/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-14144/tmp.a2m (3 sequences, 729 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14144/tmp.mod /projects/compbio/experiments/models.97/pdb/1d/1d0nA/struct-align/1d0nA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14144 tmp.script echo ReadA2M T0120-1-115.remoter-t2k.a2m.gz >> tmp.script echo PrintPrediction T0120-1-115.remoter-t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0120-1-115.remoter-t2k.2d.seq >> tmp.script echo PrintRDB T0120-1-115.remoter-t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net # command:# Reading A2M format from T0120-1-115.remoter-t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0120-1-115.remoter-t2k.a2m with 25 sequences, total weight= 13.563 avg weight= 0.542519 38 iterations Regularizing alignment for T0120-1-115.remoter-t2k.a2m.gz # After reading T0120-1-115.remoter-t2k.a2m.gz, have 115 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0120-1-115.remoter-t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0120-1-115.remoter-t2k.2d.seq # command:# Network initialization done # Printing prediction to T0120-1-115.remoter-t2k.2d.rdb # command:rm tmp.script /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0120-1-115.remoter-t2k.2d.rdb T0120-1-115.remoter-t2k-2d.mod make 1fcbA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1fcbA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1fcbA/T0120-1-115-1fcbA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-1-115.remoter-t2k-w0.5.mod,T0120-1-115.remoter-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.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 T0120-1-115.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17991/tmp.a2m T0120-1-115.remoter-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.582047 Database has 3 sequences with 1120 residues. gzip -f 1fcbA/T0120-1-115-1fcbA-2track-local.pw.a2m make 1fcbA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1fcbA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1fcbA/T0120-1-115-1fcbA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-1-115.remoter-t2k-w0.5.mod,T0120-1-115.remoter-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remoter-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.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. T0120-1-115.remoter-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17991/tmp.a2m T0120-1-115.remoter-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remoter-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 25.285978 Database has 3 sequences with 1120 residues. gzip -f 1fcbA/T0120-1-115-1fcbA-2track-global.pw.a2m make 1fcbA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1fcbA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1fcbA/T0120-1-115-1fcbA-vit.pw \ -i T0120-1-115.remoter-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remoter-t2k-w0.5.mod T0120-1-115.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17991/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: -70.724396 Database has 3 sequences with 1120 residues. gzip -f 1fcbA/T0120-1-115-1fcbA-vit.pw.a2m make[2]: Target `1fcbA/1fcbA-T0120-1-115-vit.pw.a2m.gz' not remade because of errors. make 1fcbA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1fcbA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1fcbA/T0120-1-115-1fcbA-global.pw -i T0120-1-115.remoter-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fcbA/info/1fcbA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remoter-t2k-w0.5.mod T0120-1-115.remoter-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17991/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: -7.646305 Database has 3 sequences with 1120 residues. gzip -f 1fcbA/T0120-1-115-1fcbA-global.pw.a2m make[2]: Target `1fcbA/1fcbA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1f/1fcbA/struct-align/1fcbA.fssp-w0.5.mod', needed by `1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1fcbA/xxxx-1fcbA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. rm T0120-1-115.remoter-t2k.2d.rdb make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo remote 2track remote 2track make -k PRED=1svy PRED2=1s A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1svy/T0120-1-115-1svy-local.pw.a2m.gz 1svy/1svy-T0120-1-115-local.pw.a2m.gz \ 1svy/T0120-1-115-1svy-2track-local.pw.a2m.gz \ 1svy/T0120-1-115-1svy-2track-global.pw.a2m.gz \ 1svy/T0120-1-115-1svy-vit.pw.a2m.gz 1svy/1svy-T0120-1-115-vit.pw.a2m.gz \ 1svy/T0120-1-115-1svy-global.pw.a2m.gz 1svy/1svy-T0120-1-115-global.pw.a2m.gz \ 1svy/1svy-T0120-1-115-fssp-global.pw.a2m.gz \ 1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz 1svy/xxxx-1svy-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1svy/T0120-1-115-1svy-local.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-2track-local.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-2track-global.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-vit.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-global.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1svy/xxxx-1svy-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1din PRED2=1d A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1din/T0120-1-115-1din-local.pw.a2m.gz 1din/1din-T0120-1-115-local.pw.a2m.gz \ 1din/T0120-1-115-1din-2track-local.pw.a2m.gz \ 1din/T0120-1-115-1din-2track-global.pw.a2m.gz \ 1din/T0120-1-115-1din-vit.pw.a2m.gz 1din/1din-T0120-1-115-vit.pw.a2m.gz \ 1din/T0120-1-115-1din-global.pw.a2m.gz 1din/1din-T0120-1-115-global.pw.a2m.gz \ 1din/1din-T0120-1-115-fssp-global.pw.a2m.gz \ 1din/xxxx-1din-T0120-1-115-local.pw.a2m.gz 1din/xxxx-1din-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1din/T0120-1-115-1din-local.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-2track-local.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-2track-global.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-vit.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-global.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1din/xxxx-1din-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1din/xxxx-1din-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1din/xxxx-1din-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1svr PRED2=1s A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1svr/T0120-1-115-1svr-local.pw.a2m.gz 1svr/1svr-T0120-1-115-local.pw.a2m.gz \ 1svr/T0120-1-115-1svr-2track-local.pw.a2m.gz \ 1svr/T0120-1-115-1svr-2track-global.pw.a2m.gz \ 1svr/T0120-1-115-1svr-vit.pw.a2m.gz 1svr/1svr-T0120-1-115-vit.pw.a2m.gz \ 1svr/T0120-1-115-1svr-global.pw.a2m.gz 1svr/1svr-T0120-1-115-global.pw.a2m.gz \ 1svr/1svr-T0120-1-115-fssp-global.pw.a2m.gz \ 1svr/xxxx-1svr-T0120-1-115-local.pw.a2m.gz 1svr/xxxx-1svr-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1svr/T0120-1-115-1svr-local.pw.a2m.gz' is up to date. make[2]: `1svr/1svr-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-2track-local.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-2track-global.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-vit.pw.a2m.gz' is up to date. make[2]: `1svr/1svr-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-global.pw.a2m.gz' is up to date. make[2]: `1svr/1svr-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1svr/struct-align/1svr.fssp-w0.5.mod', needed by `1svr/1svr-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1svr/1svr-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1svr/xxxx-1svr-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1svr/xxxx-1svr-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1svr/xxxx-1svr-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1azpA PRED2=1a A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1azpA/T0120-1-115-1azpA-local.pw.a2m.gz 1azpA/1azpA-T0120-1-115-local.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-2track-local.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-2track-global.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-vit.pw.a2m.gz 1azpA/1azpA-T0120-1-115-vit.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-global.pw.a2m.gz 1azpA/1azpA-T0120-1-115-global.pw.a2m.gz \ 1azpA/1azpA-T0120-1-115-fssp-global.pw.a2m.gz \ 1azpA/xxxx-1azpA-T0120-1-115-local.pw.a2m.gz 1azpA/xxxx-1azpA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1azpA/T0120-1-115-1azpA-local.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-2track-local.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-2track-global.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-vit.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-global.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1azpA/xxxx-1azpA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1azpA/xxxx-1azpA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1azpA/xxxx-1azpA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1d0nA PRED2=1d A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1d0nA/T0120-1-115-1d0nA-local.pw.a2m.gz 1d0nA/1d0nA-T0120-1-115-local.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-2track-local.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-2track-global.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-vit.pw.a2m.gz 1d0nA/1d0nA-T0120-1-115-vit.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-global.pw.a2m.gz 1d0nA/1d0nA-T0120-1-115-global.pw.a2m.gz \ 1d0nA/1d0nA-T0120-1-115-fssp-global.pw.a2m.gz \ 1d0nA/xxxx-1d0nA-T0120-1-115-local.pw.a2m.gz 1d0nA/xxxx-1d0nA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1d0nA/T0120-1-115-1d0nA-local.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-2track-local.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-2track-global.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-vit.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-global.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d0nA/xxxx-1d0nA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1d0nA/xxxx-1d0nA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1d0nA/xxxx-1d0nA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1whtA PRED2=1w A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1whtA/T0120-1-115-1whtA-local.pw.a2m.gz 1whtA/1whtA-T0120-1-115-local.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-2track-local.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-2track-global.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-vit.pw.a2m.gz 1whtA/1whtA-T0120-1-115-vit.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-global.pw.a2m.gz 1whtA/1whtA-T0120-1-115-global.pw.a2m.gz \ 1whtA/1whtA-T0120-1-115-fssp-global.pw.a2m.gz \ 1whtA/xxxx-1whtA-T0120-1-115-local.pw.a2m.gz 1whtA/xxxx-1whtA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1whtA/T0120-1-115-1whtA-local.pw.a2m.gz' is up to date. make[2]: `1whtA/1whtA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-2track-local.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-2track-global.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-vit.pw.a2m.gz' is up to date. make[2]: `1whtA/1whtA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-global.pw.a2m.gz' is up to date. make[2]: `1whtA/1whtA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1w/1whtA/struct-align/1whtA.fssp-w0.5.mod', needed by `1whtA/1whtA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1whtA/1whtA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1whtA/xxxx-1whtA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1whtA/xxxx-1whtA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1whtA/xxxx-1whtA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1ekjB PRED2=1e A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1ekjB/T0120-1-115-1ekjB-local.pw.a2m.gz 1ekjB/1ekjB-T0120-1-115-local.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-2track-local.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-2track-global.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-vit.pw.a2m.gz 1ekjB/1ekjB-T0120-1-115-vit.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-global.pw.a2m.gz 1ekjB/1ekjB-T0120-1-115-global.pw.a2m.gz \ 1ekjB/1ekjB-T0120-1-115-fssp-global.pw.a2m.gz \ 1ekjB/xxxx-1ekjB-T0120-1-115-local.pw.a2m.gz 1ekjB/xxxx-1ekjB-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1ekjB/T0120-1-115-1ekjB-local.pw.a2m.gz' is up to date. make[2]: `1ekjB/1ekjB-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-2track-local.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-2track-global.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-vit.pw.a2m.gz' is up to date. make[2]: `1ekjB/1ekjB-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-global.pw.a2m.gz' is up to date. make[2]: `1ekjB/1ekjB-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1ekjB/struct-align/1ekjB.fssp-w0.5.mod', needed by `1ekjB/1ekjB-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1ekjB/1ekjB-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ekjB/xxxx-1ekjB-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1ekjB/xxxx-1ekjB-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1ekjB/xxxx-1ekjB-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo target target make -k PRED=1ckqA PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1ckqA/T0120-1-115-1ckqA-local.pw.a2m.gz 1ckqA/1ckqA-T0120-1-115-local.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-2track-local.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-2track-global.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-vit.pw.a2m.gz 1ckqA/1ckqA-T0120-1-115-vit.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-global.pw.a2m.gz 1ckqA/1ckqA-T0120-1-115-global.pw.a2m.gz \ 1ckqA/1ckqA-T0120-1-115-fssp-global.pw.a2m.gz \ 1ckqA/xxxx-1ckqA-T0120-1-115-local.pw.a2m.gz 1ckqA/xxxx-1ckqA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1ckqA/T0120-1-115-1ckqA-local.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-2track-local.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-2track-global.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-vit.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-global.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckqA/xxxx-1ckqA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1ckqA/xxxx-1ckqA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1ckqA/xxxx-1ckqA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1a8rA PRED2=1a A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1a8rA/T0120-1-115-1a8rA-local.pw.a2m.gz 1a8rA/1a8rA-T0120-1-115-local.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-2track-local.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-2track-global.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-vit.pw.a2m.gz 1a8rA/1a8rA-T0120-1-115-vit.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-global.pw.a2m.gz 1a8rA/1a8rA-T0120-1-115-global.pw.a2m.gz \ 1a8rA/1a8rA-T0120-1-115-fssp-global.pw.a2m.gz \ 1a8rA/xxxx-1a8rA-T0120-1-115-local.pw.a2m.gz 1a8rA/xxxx-1a8rA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1a8rA/T0120-1-115-1a8rA-local.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-2track-local.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-2track-global.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-vit.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-global.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a8rA/xxxx-1a8rA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1a8rA/xxxx-1a8rA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1a8rA/xxxx-1a8rA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1cfe PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1cfe/T0120-1-115-1cfe-local.pw.a2m.gz 1cfe/1cfe-T0120-1-115-local.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-2track-local.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-2track-global.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-vit.pw.a2m.gz 1cfe/1cfe-T0120-1-115-vit.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-global.pw.a2m.gz 1cfe/1cfe-T0120-1-115-global.pw.a2m.gz \ 1cfe/1cfe-T0120-1-115-fssp-global.pw.a2m.gz \ 1cfe/xxxx-1cfe-T0120-1-115-local.pw.a2m.gz 1cfe/xxxx-1cfe-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1cfe/T0120-1-115-1cfe-local.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-2track-local.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-2track-global.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-vit.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-global.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfe/xxxx-1cfe-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1cfe/xxxx-1cfe-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1cfe/xxxx-1cfe-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo template template make -k PRED=1bs2A PRED2=1b A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1bs2A/T0120-1-115-1bs2A-local.pw.a2m.gz 1bs2A/1bs2A-T0120-1-115-local.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-2track-local.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-2track-global.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-vit.pw.a2m.gz 1bs2A/1bs2A-T0120-1-115-vit.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-global.pw.a2m.gz 1bs2A/1bs2A-T0120-1-115-global.pw.a2m.gz \ 1bs2A/1bs2A-T0120-1-115-fssp-global.pw.a2m.gz \ 1bs2A/xxxx-1bs2A-T0120-1-115-local.pw.a2m.gz 1bs2A/xxxx-1bs2A-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1bs2A/T0120-1-115-1bs2A-local.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-2track-local.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-2track-global.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-vit.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-global.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bs2A/xxxx-1bs2A-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1bs2A/xxxx-1bs2A-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1bs2A/xxxx-1bs2A-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo from full-length, same possible domain from full-length, same possible domain make -k PRED=1c4xA PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1c4xA/T0120-1-115-1c4xA-local.pw.a2m.gz 1c4xA/1c4xA-T0120-1-115-local.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-2track-local.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-2track-global.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-vit.pw.a2m.gz 1c4xA/1c4xA-T0120-1-115-vit.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-global.pw.a2m.gz 1c4xA/1c4xA-T0120-1-115-global.pw.a2m.gz \ 1c4xA/1c4xA-T0120-1-115-fssp-global.pw.a2m.gz \ 1c4xA/xxxx-1c4xA-T0120-1-115-local.pw.a2m.gz 1c4xA/xxxx-1c4xA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1c4xA/T0120-1-115-1c4xA-local.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-2track-local.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-2track-global.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-vit.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-global.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c4xA/xxxx-1c4xA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1c4xA/xxxx-1c4xA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1c4xA/xxxx-1c4xA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo remoter target remoter target make -k PRED=1fcbA PRED2=1f A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1fcbA/T0120-1-115-1fcbA-local.pw.a2m.gz 1fcbA/1fcbA-T0120-1-115-local.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-2track-local.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-2track-global.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-vit.pw.a2m.gz 1fcbA/1fcbA-T0120-1-115-vit.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-global.pw.a2m.gz 1fcbA/1fcbA-T0120-1-115-global.pw.a2m.gz \ 1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz \ 1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz 1fcbA/xxxx-1fcbA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1fcbA/T0120-1-115-1fcbA-local.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1f/1fcbA/nostruct-align/1fcbA.t99-w0.5.mod', needed by `1fcbA/1fcbA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1fcbA/1fcbA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: `1fcbA/T0120-1-115-1fcbA-2track-local.pw.a2m.gz' is up to date. make[2]: `1fcbA/T0120-1-115-1fcbA-2track-global.pw.a2m.gz' is up to date. make[2]: `1fcbA/T0120-1-115-1fcbA-vit.pw.a2m.gz' is up to date. make[2]: Target `1fcbA/1fcbA-T0120-1-115-vit.pw.a2m.gz' not remade because of errors. make[2]: `1fcbA/T0120-1-115-1fcbA-global.pw.a2m.gz' is up to date. make[2]: Target `1fcbA/1fcbA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1f/1fcbA/struct-align/1fcbA.fssp-w0.5.mod', needed by `1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1fcbA/xxxx-1fcbA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo remote 2track remote 2track make -k PRED=1svy PRED2=1s A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1svy/T0120-1-115-1svy-local.pw.a2m.gz 1svy/1svy-T0120-1-115-local.pw.a2m.gz \ 1svy/T0120-1-115-1svy-2track-local.pw.a2m.gz \ 1svy/T0120-1-115-1svy-2track-global.pw.a2m.gz \ 1svy/T0120-1-115-1svy-vit.pw.a2m.gz 1svy/1svy-T0120-1-115-vit.pw.a2m.gz \ 1svy/T0120-1-115-1svy-global.pw.a2m.gz 1svy/1svy-T0120-1-115-global.pw.a2m.gz \ 1svy/1svy-T0120-1-115-fssp-global.pw.a2m.gz \ 1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz 1svy/xxxx-1svy-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1svy/T0120-1-115-1svy-local.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-2track-local.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-2track-global.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-vit.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1svy/T0120-1-115-1svy-global.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1svy/1svy-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1svy/xxxx-1svy-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1svy/xxxx-1svy-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1din PRED2=1d A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1din/T0120-1-115-1din-local.pw.a2m.gz 1din/1din-T0120-1-115-local.pw.a2m.gz \ 1din/T0120-1-115-1din-2track-local.pw.a2m.gz \ 1din/T0120-1-115-1din-2track-global.pw.a2m.gz \ 1din/T0120-1-115-1din-vit.pw.a2m.gz 1din/1din-T0120-1-115-vit.pw.a2m.gz \ 1din/T0120-1-115-1din-global.pw.a2m.gz 1din/1din-T0120-1-115-global.pw.a2m.gz \ 1din/1din-T0120-1-115-fssp-global.pw.a2m.gz \ 1din/xxxx-1din-T0120-1-115-local.pw.a2m.gz 1din/xxxx-1din-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1din/T0120-1-115-1din-local.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-2track-local.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-2track-global.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-vit.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1din/T0120-1-115-1din-global.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1din/1din-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1din/xxxx-1din-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1din/xxxx-1din-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1din/xxxx-1din-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1svr PRED2=1s A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1svr/T0120-1-115-1svr-local.pw.a2m.gz 1svr/1svr-T0120-1-115-local.pw.a2m.gz \ 1svr/T0120-1-115-1svr-2track-local.pw.a2m.gz \ 1svr/T0120-1-115-1svr-2track-global.pw.a2m.gz \ 1svr/T0120-1-115-1svr-vit.pw.a2m.gz 1svr/1svr-T0120-1-115-vit.pw.a2m.gz \ 1svr/T0120-1-115-1svr-global.pw.a2m.gz 1svr/1svr-T0120-1-115-global.pw.a2m.gz \ 1svr/1svr-T0120-1-115-fssp-global.pw.a2m.gz \ 1svr/xxxx-1svr-T0120-1-115-local.pw.a2m.gz 1svr/xxxx-1svr-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1svr/T0120-1-115-1svr-local.pw.a2m.gz' is up to date. make[2]: `1svr/1svr-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-2track-local.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-2track-global.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-vit.pw.a2m.gz' is up to date. make[2]: `1svr/1svr-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1svr/T0120-1-115-1svr-global.pw.a2m.gz' is up to date. make[2]: `1svr/1svr-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1svr/struct-align/1svr.fssp-w0.5.mod', needed by `1svr/1svr-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1svr/1svr-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1svr/xxxx-1svr-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1svr/xxxx-1svr-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1svr/xxxx-1svr-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1azpA PRED2=1a A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1azpA/T0120-1-115-1azpA-local.pw.a2m.gz 1azpA/1azpA-T0120-1-115-local.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-2track-local.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-2track-global.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-vit.pw.a2m.gz 1azpA/1azpA-T0120-1-115-vit.pw.a2m.gz \ 1azpA/T0120-1-115-1azpA-global.pw.a2m.gz 1azpA/1azpA-T0120-1-115-global.pw.a2m.gz \ 1azpA/1azpA-T0120-1-115-fssp-global.pw.a2m.gz \ 1azpA/xxxx-1azpA-T0120-1-115-local.pw.a2m.gz 1azpA/xxxx-1azpA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1azpA/T0120-1-115-1azpA-local.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-2track-local.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-2track-global.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-vit.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1azpA/T0120-1-115-1azpA-global.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1azpA/1azpA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1azpA/xxxx-1azpA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1azpA/xxxx-1azpA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1azpA/xxxx-1azpA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1d0nA PRED2=1d A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1d0nA/T0120-1-115-1d0nA-local.pw.a2m.gz 1d0nA/1d0nA-T0120-1-115-local.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-2track-local.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-2track-global.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-vit.pw.a2m.gz 1d0nA/1d0nA-T0120-1-115-vit.pw.a2m.gz \ 1d0nA/T0120-1-115-1d0nA-global.pw.a2m.gz 1d0nA/1d0nA-T0120-1-115-global.pw.a2m.gz \ 1d0nA/1d0nA-T0120-1-115-fssp-global.pw.a2m.gz \ 1d0nA/xxxx-1d0nA-T0120-1-115-local.pw.a2m.gz 1d0nA/xxxx-1d0nA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1d0nA/T0120-1-115-1d0nA-local.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-2track-local.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-2track-global.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-vit.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1d0nA/T0120-1-115-1d0nA-global.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1d0nA/1d0nA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d0nA/xxxx-1d0nA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1d0nA/xxxx-1d0nA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1d0nA/xxxx-1d0nA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1whtA PRED2=1w A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1whtA/T0120-1-115-1whtA-local.pw.a2m.gz 1whtA/1whtA-T0120-1-115-local.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-2track-local.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-2track-global.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-vit.pw.a2m.gz 1whtA/1whtA-T0120-1-115-vit.pw.a2m.gz \ 1whtA/T0120-1-115-1whtA-global.pw.a2m.gz 1whtA/1whtA-T0120-1-115-global.pw.a2m.gz \ 1whtA/1whtA-T0120-1-115-fssp-global.pw.a2m.gz \ 1whtA/xxxx-1whtA-T0120-1-115-local.pw.a2m.gz 1whtA/xxxx-1whtA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1whtA/T0120-1-115-1whtA-local.pw.a2m.gz' is up to date. make[2]: `1whtA/1whtA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-2track-local.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-2track-global.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-vit.pw.a2m.gz' is up to date. make[2]: `1whtA/1whtA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1whtA/T0120-1-115-1whtA-global.pw.a2m.gz' is up to date. make[2]: `1whtA/1whtA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1w/1whtA/struct-align/1whtA.fssp-w0.5.mod', needed by `1whtA/1whtA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1whtA/1whtA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1whtA/xxxx-1whtA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1whtA/xxxx-1whtA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1whtA/xxxx-1whtA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1ekjB PRED2=1e A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1ekjB/T0120-1-115-1ekjB-local.pw.a2m.gz 1ekjB/1ekjB-T0120-1-115-local.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-2track-local.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-2track-global.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-vit.pw.a2m.gz 1ekjB/1ekjB-T0120-1-115-vit.pw.a2m.gz \ 1ekjB/T0120-1-115-1ekjB-global.pw.a2m.gz 1ekjB/1ekjB-T0120-1-115-global.pw.a2m.gz \ 1ekjB/1ekjB-T0120-1-115-fssp-global.pw.a2m.gz \ 1ekjB/xxxx-1ekjB-T0120-1-115-local.pw.a2m.gz 1ekjB/xxxx-1ekjB-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1ekjB/T0120-1-115-1ekjB-local.pw.a2m.gz' is up to date. make[2]: `1ekjB/1ekjB-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-2track-local.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-2track-global.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-vit.pw.a2m.gz' is up to date. make[2]: `1ekjB/1ekjB-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1ekjB/T0120-1-115-1ekjB-global.pw.a2m.gz' is up to date. make[2]: `1ekjB/1ekjB-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1ekjB/struct-align/1ekjB.fssp-w0.5.mod', needed by `1ekjB/1ekjB-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1ekjB/1ekjB-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ekjB/xxxx-1ekjB-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1ekjB/xxxx-1ekjB-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1ekjB/xxxx-1ekjB-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo target target make -k PRED=1ckqA PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1ckqA/T0120-1-115-1ckqA-local.pw.a2m.gz 1ckqA/1ckqA-T0120-1-115-local.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-2track-local.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-2track-global.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-vit.pw.a2m.gz 1ckqA/1ckqA-T0120-1-115-vit.pw.a2m.gz \ 1ckqA/T0120-1-115-1ckqA-global.pw.a2m.gz 1ckqA/1ckqA-T0120-1-115-global.pw.a2m.gz \ 1ckqA/1ckqA-T0120-1-115-fssp-global.pw.a2m.gz \ 1ckqA/xxxx-1ckqA-T0120-1-115-local.pw.a2m.gz 1ckqA/xxxx-1ckqA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1ckqA/T0120-1-115-1ckqA-local.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-2track-local.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-2track-global.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-vit.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1ckqA/T0120-1-115-1ckqA-global.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1ckqA/1ckqA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckqA/xxxx-1ckqA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1ckqA/xxxx-1ckqA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1ckqA/xxxx-1ckqA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1a8rA PRED2=1a A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1a8rA/T0120-1-115-1a8rA-local.pw.a2m.gz 1a8rA/1a8rA-T0120-1-115-local.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-2track-local.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-2track-global.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-vit.pw.a2m.gz 1a8rA/1a8rA-T0120-1-115-vit.pw.a2m.gz \ 1a8rA/T0120-1-115-1a8rA-global.pw.a2m.gz 1a8rA/1a8rA-T0120-1-115-global.pw.a2m.gz \ 1a8rA/1a8rA-T0120-1-115-fssp-global.pw.a2m.gz \ 1a8rA/xxxx-1a8rA-T0120-1-115-local.pw.a2m.gz 1a8rA/xxxx-1a8rA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1a8rA/T0120-1-115-1a8rA-local.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-2track-local.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-2track-global.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-vit.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1a8rA/T0120-1-115-1a8rA-global.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1a8rA/1a8rA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a8rA/xxxx-1a8rA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1a8rA/xxxx-1a8rA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1a8rA/xxxx-1a8rA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1cfe PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1cfe/T0120-1-115-1cfe-local.pw.a2m.gz 1cfe/1cfe-T0120-1-115-local.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-2track-local.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-2track-global.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-vit.pw.a2m.gz 1cfe/1cfe-T0120-1-115-vit.pw.a2m.gz \ 1cfe/T0120-1-115-1cfe-global.pw.a2m.gz 1cfe/1cfe-T0120-1-115-global.pw.a2m.gz \ 1cfe/1cfe-T0120-1-115-fssp-global.pw.a2m.gz \ 1cfe/xxxx-1cfe-T0120-1-115-local.pw.a2m.gz 1cfe/xxxx-1cfe-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1cfe/T0120-1-115-1cfe-local.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-2track-local.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-2track-global.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-vit.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1cfe/T0120-1-115-1cfe-global.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1cfe/1cfe-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfe/xxxx-1cfe-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1cfe/xxxx-1cfe-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1cfe/xxxx-1cfe-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo template template make -k PRED=1bs2A PRED2=1b A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1bs2A/T0120-1-115-1bs2A-local.pw.a2m.gz 1bs2A/1bs2A-T0120-1-115-local.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-2track-local.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-2track-global.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-vit.pw.a2m.gz 1bs2A/1bs2A-T0120-1-115-vit.pw.a2m.gz \ 1bs2A/T0120-1-115-1bs2A-global.pw.a2m.gz 1bs2A/1bs2A-T0120-1-115-global.pw.a2m.gz \ 1bs2A/1bs2A-T0120-1-115-fssp-global.pw.a2m.gz \ 1bs2A/xxxx-1bs2A-T0120-1-115-local.pw.a2m.gz 1bs2A/xxxx-1bs2A-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1bs2A/T0120-1-115-1bs2A-local.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-2track-local.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-2track-global.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-vit.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1bs2A/T0120-1-115-1bs2A-global.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1bs2A/1bs2A-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bs2A/xxxx-1bs2A-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1bs2A/xxxx-1bs2A-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1bs2A/xxxx-1bs2A-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo from full-length, same possible domain from full-length, same possible domain make -k PRED=1c4xA PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1c4xA/T0120-1-115-1c4xA-local.pw.a2m.gz 1c4xA/1c4xA-T0120-1-115-local.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-2track-local.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-2track-global.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-vit.pw.a2m.gz 1c4xA/1c4xA-T0120-1-115-vit.pw.a2m.gz \ 1c4xA/T0120-1-115-1c4xA-global.pw.a2m.gz 1c4xA/1c4xA-T0120-1-115-global.pw.a2m.gz \ 1c4xA/1c4xA-T0120-1-115-fssp-global.pw.a2m.gz \ 1c4xA/xxxx-1c4xA-T0120-1-115-local.pw.a2m.gz 1c4xA/xxxx-1c4xA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1c4xA/T0120-1-115-1c4xA-local.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-local.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-2track-local.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-2track-global.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-vit.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-vit.pw.a2m.gz' is up to date. make[2]: `1c4xA/T0120-1-115-1c4xA-global.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-global.pw.a2m.gz' is up to date. make[2]: `1c4xA/1c4xA-T0120-1-115-fssp-global.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c4xA/xxxx-1c4xA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1c4xA/xxxx-1c4xA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1c4xA/xxxx-1c4xA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo remoter target remoter target make -k PRED=1fcbA PRED2=1f A2M=remoter-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1fcbA/T0120-1-115-1fcbA-local.pw.a2m.gz 1fcbA/1fcbA-T0120-1-115-local.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-2track-local.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-2track-global.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-vit.pw.a2m.gz 1fcbA/1fcbA-T0120-1-115-vit.pw.a2m.gz \ 1fcbA/T0120-1-115-1fcbA-global.pw.a2m.gz 1fcbA/1fcbA-T0120-1-115-global.pw.a2m.gz \ 1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz \ 1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz 1fcbA/xxxx-1fcbA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[2]: `1fcbA/T0120-1-115-1fcbA-local.pw.a2m.gz' is up to date. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1f/1fcbA/nostruct-align/1fcbA.t99-w0.5.mod', needed by `1fcbA/1fcbA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1fcbA/1fcbA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: `1fcbA/T0120-1-115-1fcbA-2track-local.pw.a2m.gz' is up to date. make[2]: `1fcbA/T0120-1-115-1fcbA-2track-global.pw.a2m.gz' is up to date. make[2]: `1fcbA/T0120-1-115-1fcbA-vit.pw.a2m.gz' is up to date. make[2]: Target `1fcbA/1fcbA-T0120-1-115-vit.pw.a2m.gz' not remade because of errors. make[2]: `1fcbA/T0120-1-115-1fcbA-global.pw.a2m.gz' is up to date. make[2]: Target `1fcbA/1fcbA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1f/1fcbA/struct-align/1fcbA.fssp-w0.5.mod', needed by `1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1fcbA/1fcbA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1fcbA/xxxx-1fcbA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1fcbA/xxxx-1fcbA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) echo remoter 2track remoter 2track make -k PRED=1cleA PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1cleA/T0120-1-115-1cleA-local.pw.a2m.gz 1cleA/1cleA-T0120-1-115-local.pw.a2m.gz \ 1cleA/T0120-1-115-1cleA-2track-local.pw.a2m.gz \ 1cleA/T0120-1-115-1cleA-2track-global.pw.a2m.gz \ 1cleA/T0120-1-115-1cleA-vit.pw.a2m.gz 1cleA/1cleA-T0120-1-115-vit.pw.a2m.gz \ 1cleA/T0120-1-115-1cleA-global.pw.a2m.gz 1cleA/1cleA-T0120-1-115-global.pw.a2m.gz \ 1cleA/1cleA-T0120-1-115-fssp-global.pw.a2m.gz \ 1cleA/xxxx-1cleA-T0120-1-115-local.pw.a2m.gz 1cleA/xxxx-1cleA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' mkdir 1cleA fixmode 1cleA make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/T0120-1-115-1cleA-local.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -66.005722 Database has 3 sequences with 1183 residues. gzip -f 1cleA/T0120-1-115-1cleA-local.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/1cleA-T0120-1-115-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22723/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: -239.001785 Database has 3 sequences with 1183 residues. gzip -f 1cleA/1cleA-T0120-1-115-local.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/T0120-1-115-1cleA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.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 T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.508102 Database has 3 sequences with 1183 residues. gzip -f 1cleA/T0120-1-115-1cleA-2track-local.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/T0120-1-115-1cleA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.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. T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 23.187296 Database has 3 sequences with 1183 residues. gzip -f 1cleA/T0120-1-115-1cleA-2track-global.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/T0120-1-115-1cleA-vit.pw \ -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -61.746387 Database has 3 sequences with 1183 residues. gzip -f 1cleA/T0120-1-115-1cleA-vit.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/1cleA-T0120-1-115-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22723/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: -233.902084 Database has 3 sequences with 1183 residues. gzip -f 1cleA/1cleA-T0120-1-115-vit.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/T0120-1-115-1cleA-global.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: 8.538006 Database has 3 sequences with 1183 residues. gzip -f 1cleA/T0120-1-115-1cleA-global.pw.a2m make 1cleA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cleA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cleA/1cleA-T0120-1-115-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cleA/info/1cleA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cleA/nostruct-align/1cleA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22723/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: -225.063370 Database has 3 sequences with 1183 residues. gzip -f 1cleA/1cleA-T0120-1-115-global.pw.a2m make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1cleA/struct-align/1cleA.fssp-w0.5.mod', needed by `1cleA/1cleA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1cleA/1cleA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cleA/xxxx-1cleA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1cleA/xxxx-1cleA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1cleA/xxxx-1cleA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1crl PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1crl/T0120-1-115-1crl-local.pw.a2m.gz 1crl/1crl-T0120-1-115-local.pw.a2m.gz \ 1crl/T0120-1-115-1crl-2track-local.pw.a2m.gz \ 1crl/T0120-1-115-1crl-2track-global.pw.a2m.gz \ 1crl/T0120-1-115-1crl-vit.pw.a2m.gz 1crl/1crl-T0120-1-115-vit.pw.a2m.gz \ 1crl/T0120-1-115-1crl-global.pw.a2m.gz 1crl/1crl-T0120-1-115-global.pw.a2m.gz \ 1crl/1crl-T0120-1-115-fssp-global.pw.a2m.gz \ 1crl/xxxx-1crl-T0120-1-115-local.pw.a2m.gz 1crl/xxxx-1crl-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' mkdir 1crl fixmode 1crl make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/T0120-1-115-1crl-local.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -65.966446 Database has 3 sequences with 1183 residues. gzip -f 1crl/T0120-1-115-1crl-local.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/1crl-T0120-1-115-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16110/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: -250.016403 Database has 3 sequences with 1183 residues. gzip -f 1crl/1crl-T0120-1-115-local.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/T0120-1-115-1crl-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.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 T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -51.969090 Database has 3 sequences with 1183 residues. gzip -f 1crl/T0120-1-115-1crl-2track-local.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/T0120-1-115-1crl-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.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. T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 23.752356 Database has 3 sequences with 1183 residues. gzip -f 1crl/T0120-1-115-1crl-2track-global.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/T0120-1-115-1crl-vit.pw \ -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -61.545734 Database has 3 sequences with 1183 residues. gzip -f 1crl/T0120-1-115-1crl-vit.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/1crl-T0120-1-115-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16110/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: -245.424088 Database has 3 sequences with 1183 residues. gzip -f 1crl/1crl-T0120-1-115-vit.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/T0120-1-115-1crl-global.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: 8.286678 Database has 3 sequences with 1183 residues. gzip -f 1crl/T0120-1-115-1crl-global.pw.a2m make 1crl make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1crl' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1crl/1crl-T0120-1-115-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1crl/info/1crl.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1crl/nostruct-align/1crl.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16110/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: -237.247360 Database has 3 sequences with 1183 residues. gzip -f 1crl/1crl-T0120-1-115-global.pw.a2m make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1crl/struct-align/1crl.fssp-w0.5.mod', needed by `1crl/1crl-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1crl/1crl-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1crl/xxxx-1crl-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1crl/xxxx-1crl-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1crl/xxxx-1crl-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1qjwA PRED2=1q A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1qjwA/T0120-1-115-1qjwA-local.pw.a2m.gz 1qjwA/1qjwA-T0120-1-115-local.pw.a2m.gz \ 1qjwA/T0120-1-115-1qjwA-2track-local.pw.a2m.gz \ 1qjwA/T0120-1-115-1qjwA-2track-global.pw.a2m.gz \ 1qjwA/T0120-1-115-1qjwA-vit.pw.a2m.gz 1qjwA/1qjwA-T0120-1-115-vit.pw.a2m.gz \ 1qjwA/T0120-1-115-1qjwA-global.pw.a2m.gz 1qjwA/1qjwA-T0120-1-115-global.pw.a2m.gz \ 1qjwA/1qjwA-T0120-1-115-fssp-global.pw.a2m.gz \ 1qjwA/xxxx-1qjwA-T0120-1-115-local.pw.a2m.gz 1qjwA/xxxx-1qjwA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' mkdir 1qjwA fixmode 1qjwA make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/T0120-1-115-1qjwA-local.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -66.282822 Database has 3 sequences with 842 residues. gzip -f 1qjwA/T0120-1-115-1qjwA-local.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/1qjwA-T0120-1-115-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30979/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: -235.392502 Database has 3 sequences with 842 residues. gzip -f 1qjwA/1qjwA-T0120-1-115-local.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/T0120-1-115-1qjwA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.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 T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -51.230854 Database has 3 sequences with 842 residues. gzip -f 1qjwA/T0120-1-115-1qjwA-2track-local.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/T0120-1-115-1qjwA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.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. T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -2.032011 Database has 3 sequences with 842 residues. gzip -f 1qjwA/T0120-1-115-1qjwA-2track-global.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/T0120-1-115-1qjwA-vit.pw \ -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -62.556168 Database has 3 sequences with 842 residues. gzip -f 1qjwA/T0120-1-115-1qjwA-vit.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/1qjwA-T0120-1-115-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30979/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: -232.002487 Database has 3 sequences with 842 residues. gzip -f 1qjwA/1qjwA-T0120-1-115-vit.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/T0120-1-115-1qjwA-global.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -16.914642 Database has 3 sequences with 842 residues. gzip -f 1qjwA/T0120-1-115-1qjwA-global.pw.a2m make 1qjwA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1qjwA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1qjwA/1qjwA-T0120-1-115-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qjwA/info/1qjwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qjwA/nostruct-align/1qjwA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30979/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: -222.857666 Database has 3 sequences with 842 residues. gzip -f 1qjwA/1qjwA-T0120-1-115-global.pw.a2m make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qjwA/struct-align/1qjwA.fssp-w0.5.mod', needed by `1qjwA/1qjwA-T0120-1-115-fssp-global.pw.a2m.gz'. make[2]: Target `1qjwA/1qjwA-T0120-1-115-fssp-global.pw.a2m.gz' not remade because of errors. make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qjwA/xxxx-1qjwA-T0120-1-115-local.pw.a2m.gz'. make[2]: Target `1qjwA/xxxx-1qjwA-T0120-1-115-local.pw.a2m.gz' not remade because of errors. make[2]: Target `1qjwA/xxxx-1qjwA-T0120-1-115-global.pw.a2m.gz' not remade because of errors. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[1]: *** [joint] Error 2 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make: [joints] Error 2 (ignored) make -k PRED=1cozA PRED2=1c A2M=remote-t2k.a2m.gz joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make -k \ 1cozA/T0120-1-115-1cozA-local.pw.a2m.gz 1cozA/1cozA-T0120-1-115-local.pw.a2m.gz \ 1cozA/T0120-1-115-1cozA-2track-local.pw.a2m.gz \ 1cozA/T0120-1-115-1cozA-2track-global.pw.a2m.gz \ 1cozA/T0120-1-115-1cozA-vit.pw.a2m.gz 1cozA/1cozA-T0120-1-115-vit.pw.a2m.gz \ 1cozA/T0120-1-115-1cozA-global.pw.a2m.gz 1cozA/1cozA-T0120-1-115-global.pw.a2m.gz \ 1cozA/1cozA-T0120-1-115-fssp-global.pw.a2m.gz \ 1cozA/xxxx-1cozA-T0120-1-115-local.pw.a2m.gz 1cozA/xxxx-1cozA-T0120-1-115-global.pw.a2m.gz make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' mkdir 1cozA fixmode 1cozA make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/T0120-1-115-1cozA-local.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -66.236320 Database has 3 sequences with 370 residues. gzip -f 1cozA/T0120-1-115-1cozA-local.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/1cozA-T0120-1-115-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6533/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: -71.724991 Database has 3 sequences with 370 residues. gzip -f 1cozA/1cozA-T0120-1-115-local.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/T0120-1-115-1cozA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.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 T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -51.509491 Database has 3 sequences with 370 residues. gzip -f 1cozA/T0120-1-115-1cozA-2track-local.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/T0120-1-115-1cozA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0120-1-115.remote-t2k-w0.5.mod,T0120-1-115.remote-t2k-2d.mod \ -db T0120-1-115.seq,T0120-1-115.remote-t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.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. T0120-1-115.remote-t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/tmp.a2m T0120-1-115.remote-t2k-2d.mod(719): Reading track 1 model from MODEL -- Model from 2nd structure file T0120-1-115.remote-t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -42.909504 Database has 3 sequences with 370 residues. gzip -f 1cozA/T0120-1-115-1cozA-2track-global.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/T0120-1-115-1cozA-vit.pw \ -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -62.920658 Database has 3 sequences with 370 residues. gzip -f 1cozA/T0120-1-115-1cozA-vit.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/1cozA-T0120-1-115-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6533/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: -68.960320 Database has 3 sequences with 370 residues. gzip -f 1cozA/1cozA-T0120-1-115-vit.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/T0120-1-115-1cozA-global.pw -i T0120-1-115.remote-t2k-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0120-1-115.remote-t2k-w0.5.mod T0120-1-115.remote-t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22580/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: -58.972660 Database has 3 sequences with 370 residues. gzip -f 1cozA/T0120-1-115-1cozA-global.pw.a2m make 1cozA make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' make[3]: `1cozA' is up to date. make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120/t120-1-115' /projects/compbio/bin/alpha.new/hmmscore 1cozA/1cozA-T0120-1-115-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod -db T0120-1-115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cozA/info/1cozA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cozA/nostruct-align/1cozA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6533/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: -67.058998 Database has 3 sequences with 370 residues. gzip -f 1cozA/1cozA-T0120-1-115-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cozA/struct-align/1cozA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cozA/struct-align/1cozA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15628 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15628/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1cozA/struct-align/1cozA.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/1cozA/struct-align/1cozA.fssp.a2m.gz (10 sequences, 126 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15628/tmp.a2m. Dropping 1 (of 10) duplicate sequences with differing IDs 9 sequences left after dropping 1 of 10 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15628/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15628/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-15628/tmp.a2m (9 sequences, 126 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15628/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cozA/struct-align/1cozA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15628