make -k und/T0086-1atiA-local.index und/1atiA-T0086-local.index
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[1]: [und/T0086-1atiA-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[1]: [und/T0086-1atiA-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1atiA/T0086-1atiA-local.pw.a2m.gz \
	-target T0086 -template 1atiA \
	-out T0086-1atiA-local -outdir und
Sequence named 1atiA has all gap columns.
It will be included anyway.
Sequence named 1atiA has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1atiA-orig.a2m
Writing a2m file: tmp/1atiA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5076


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/tmp -alignfile tmp/1atiA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file tmp/1atiA-orig.a2m (1 sequences, 505 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/tmp.a2m (1 sequences, 505 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/tmp.mod tmp/1atiA-align.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1atiA-align.mod
tmp/1atiA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5076/tmp.a2m
SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05
Sequence Files:  tmp/1atiA-orig.a2m tmp/1atiA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1atiA-align.mod
Running w0.5 tmp/1atiA-orig.a2m tmp/1atiA-align.mod
Running align2model tmp/1atiA-align -i tmp/1atiA-align.mod -db tmp/1atiA-orig.a2m -db tmp/1atiA-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[1]: [und/1atiA-T0086-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[1]: [und/1atiA-T0086-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1atiA/1atiA-T0086-local.pw.a2m.gz \
	-target T0086 -template 1atiA \
	-out 1atiA-T0086-local -outdir und
Sequence named T0086 has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1atiA-orig.a2m
Writing a2m file: tmp/1atiA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27964


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/tmp -alignfile tmp/1atiA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59
Reading alignment file tmp/1atiA-orig.a2m (1 sequences, 505 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/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 (June, 2000) compiled 07/06/00_15:43:15
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/tmp.a2m (1 sequences, 505 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/tmp.mod tmp/1atiA-align.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1atiA-align.mod
tmp/1atiA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27964/tmp.a2m
SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05
Sequence Files:  tmp/1atiA-orig.a2m tmp/1atiA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1atiA-align.mod
Running w0.5 tmp/1atiA-orig.a2m tmp/1atiA-align.mod
Running align2model tmp/1atiA-align -i tmp/1atiA-align.mod -db tmp/1atiA-orig.a2m -db tmp/1atiA-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'