/projects/compbio/bin/scripts/w0.5 T0120-211-end.t2k.a2m.gz T0120-211-end.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15170 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15170/tmp -alignfile T0120-211-end.t2k.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 T0120-211-end.t2k.a2m.gz (3 sequences, 126 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15170/tmp.a2m. Dropping 1 (of 3) duplicate sequences with differing IDs Dropping 1 (of 3) sequences with > 80.0% id 1 sequences left after dropping 2 of 3 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15170/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15170/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-15170/tmp.a2m (1 sequences, 126 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15170/tmp.mod T0120-211-end.t2k-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15170 tmp.script echo ReadA2M T0120-211-end.remote-t2k.a2m.gz >> tmp.script echo PrintPrediction T0120-211-end.remote-t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0120-211-end.remote-t2k.2d.seq >> tmp.script echo PrintRDB T0120-211-end.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 T0120-211-end.remote-t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0120-211-end.remote-t2k.a2m with 11 sequences, total weight= 6.23127 avg weight= 0.566479 34 iterations Regularizing alignment for T0120-211-end.remote-t2k.a2m.gz # After reading T0120-211-end.remote-t2k.a2m.gz, have 126 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 T0120-211-end.remote-t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0120-211-end.remote-t2k.2d.seq # command:# Network initialization done # Printing prediction to T0120-211-end.remote-t2k.2d.rdb # command:rm tmp.script /projects/compbio/bin/scripts/w0.5 T0120-211-end.remote-t2k.a2m.gz T0120-211-end.remote-t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7418 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp -alignfile T0120-211-end.remote-t2k.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 T0120-211-end.remote-t2k.a2m.gz (11 sequences, 126 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.a2m. Dropping 3 (of 11) duplicate sequences with differing IDs Dropping 3 (of 11) duplicate sequences with identical IDs Dropping 1 (of 11) sequences with > 80.0% id 6 sequences left after dropping 5 of 11 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/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-7418/tmp.a2m (6 sequences, 126 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7418/tmp.mod T0120-211-end.remote-t2k-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7418