make: *** No rule to make target `T0120-1-115.remoter-t2k-2track.dist'.  Stop.
/projects/compbio/bin/scripts/w0.5 T0120-116-210.remoter-t2k.a2m.gz T0120-116-210.remoter-t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12073


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12073/tmp -alignfile T0120-116-210.remoter-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 T0120-116-210.remoter-t2k.a2m.gz (32 sequences, 95 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12073/tmp.a2m.
Dropping 15 (of 32) duplicate sequences with differing IDs
Dropping 8 (of 32) sequences with > 80.0% id
9 sequences left after dropping 23 of 32 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12073/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12073/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-12073/tmp.a2m (9 sequences, 95 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12073/tmp.mod T0120-116-210.remoter-t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12073 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confecho 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 T0120-116-210.remoter-t2k.a2m.gz >> tmp.script
echo PrintPrediction T0120-116-210.remoter-t2k.2d 3670-4530-6947 >> tmp.script
echo PrintPredictionFasta T0120-116-210.remoter-t2k.2d.seq >> tmp.script
echo PrintRDB T0120-116-210.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 T0120-116-210.remoter-t2k.a2m.gz
# Using SequenceWeight EntropyWeight(1.4, 10)
# Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer.
# T0120-116-210.remoter-t2k.a2m with 32 sequences, total weight= 13.0256 avg weight= 0.407049 30 iterations
Regularizing alignment for T0120-116-210.remoter-t2k.a2m.gz
# After reading T0120-116-210.remoter-t2k.a2m.gz, have 95 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 T0120-116-210.remoter-t2k.2d
# command:# Network initialization done
# Printing prediction  in FASTA format to T0120-116-210.remoter-t2k.2d.seq
# command:# Network initialization done
# Printing prediction to T0120-116-210.remoter-t2k.2d.rdb
# command:rm tmp.script
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0120-116-210.remoter-t2k.2d.rdb T0120-116-210.remoter-t2k-2d.mod
/projects/compbio/bin/alpha.new/hmmscore T0120-116-210.remoter-t2k-2track \
	-trackmod T0120-116-210.remoter-t2k-w0.5.mod,T0120-116-210.remoter-t2k-2d.mod \
	-db /projects/compbio/experiments/models.97/indexes/t99.seqs,/projects/compbio/experiments/models.97/indexes/t99.2ds \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -dpstyle 0 \
	-select_score 4 -Emax 40.
SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39
T0120-116-210.remoter-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12073/tmp.a2m
T0120-116-210.remoter-t2k-2d.mod(599):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120-116-210.remoter-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
....
Average NLL-Simple NULL score:        -10.898814
Database has 3507 sequences with 789089 residues.
rm T0120-116-210.remoter-t2k.2d.rdb T0120-116-210.remoter-t2k-2d.mod