make: Nothing to be done for `joints'.
make: Nothing to be done for `joints'.
make: Nothing to be done for `joints'.
make: Nothing to be done for `joints'.
make: Nothing to be done for `joints'.
echo template
template
make -k PRED=1quuA PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1quuA/T0120-1quuA-local.pw.a2m.gz 1quuA/1quuA-T0120-local.pw.a2m.gz \
1quuA/T0120-1quuA-2track-local.pw.a2m.gz \
1quuA/T0120-1quuA-2track-global.pw.a2m.gz \
1quuA/T0120-1quuA-vit.pw.a2m.gz 1quuA/1quuA-T0120-vit.pw.a2m.gz \
1quuA/T0120-1quuA-global.pw.a2m.gz 	1quuA/1quuA-T0120-global.pw.a2m.gz \
1quuA/1quuA-T0120-fssp-global.pw.a2m.gz \
1quuA/xxxx-1quuA-T0120-local.pw.a2m.gz 1quuA/xxxx-1quuA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1quuA/T0120-1quuA-local.pw.a2m.gz' is up to date.
make[2]: `1quuA/1quuA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1quuA/T0120-1quuA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1quuA/T0120-1quuA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1quuA/T0120-1quuA-vit.pw.a2m.gz' is up to date.
make[2]: `1quuA/1quuA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1quuA/T0120-1quuA-global.pw.a2m.gz' is up to date.
make[2]: `1quuA/1quuA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1quuA/1quuA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1quuA/xxxx-1quuA-T0120-local.pw.a2m.gz'.
make[2]: Target `1quuA/xxxx-1quuA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1quuA/xxxx-1quuA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1kvs  PRED2=1k joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1kvs/T0120-1kvs-local.pw.a2m.gz 1kvs/1kvs-T0120-local.pw.a2m.gz \
1kvs/T0120-1kvs-2track-local.pw.a2m.gz \
1kvs/T0120-1kvs-2track-global.pw.a2m.gz \
1kvs/T0120-1kvs-vit.pw.a2m.gz 1kvs/1kvs-T0120-vit.pw.a2m.gz \
1kvs/T0120-1kvs-global.pw.a2m.gz 	1kvs/1kvs-T0120-global.pw.a2m.gz \
1kvs/1kvs-T0120-fssp-global.pw.a2m.gz \
1kvs/xxxx-1kvs-T0120-local.pw.a2m.gz 1kvs/xxxx-1kvs-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1kvs/T0120-1kvs-local.pw.a2m.gz' is up to date.
make[2]: `1kvs/1kvs-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1kvs/T0120-1kvs-2track-local.pw.a2m.gz' is up to date.
make[2]: `1kvs/T0120-1kvs-2track-global.pw.a2m.gz' is up to date.
make[2]: `1kvs/T0120-1kvs-vit.pw.a2m.gz' is up to date.
make[2]: `1kvs/1kvs-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1kvs/T0120-1kvs-global.pw.a2m.gz' is up to date.
make[2]: `1kvs/1kvs-T0120-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kvs/struct-align/1kvs.fssp-w0.5.mod', needed by `1kvs/1kvs-T0120-fssp-global.pw.a2m.gz'.
make[2]: Target `1kvs/1kvs-T0120-fssp-global.pw.a2m.gz' not remade because of errors.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kvs/xxxx-1kvs-T0120-local.pw.a2m.gz'.
make[2]: Target `1kvs/xxxx-1kvs-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1kvs/xxxx-1kvs-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1c8zA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1c8zA/T0120-1c8zA-local.pw.a2m.gz 1c8zA/1c8zA-T0120-local.pw.a2m.gz \
1c8zA/T0120-1c8zA-2track-local.pw.a2m.gz \
1c8zA/T0120-1c8zA-2track-global.pw.a2m.gz \
1c8zA/T0120-1c8zA-vit.pw.a2m.gz 1c8zA/1c8zA-T0120-vit.pw.a2m.gz \
1c8zA/T0120-1c8zA-global.pw.a2m.gz 	1c8zA/1c8zA-T0120-global.pw.a2m.gz \
1c8zA/1c8zA-T0120-fssp-global.pw.a2m.gz \
1c8zA/xxxx-1c8zA-T0120-local.pw.a2m.gz 1c8zA/xxxx-1c8zA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1c8zA/T0120-1c8zA-local.pw.a2m.gz' is up to date.
make[2]: `1c8zA/1c8zA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1c8zA/T0120-1c8zA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1c8zA/T0120-1c8zA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1c8zA/T0120-1c8zA-vit.pw.a2m.gz' is up to date.
make[2]: `1c8zA/1c8zA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1c8zA/T0120-1c8zA-global.pw.a2m.gz' is up to date.
make[2]: `1c8zA/1c8zA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1c8zA/1c8zA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c8zA/xxxx-1c8zA-T0120-local.pw.a2m.gz'.
make[2]: Target `1c8zA/xxxx-1c8zA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1c8zA/xxxx-1c8zA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo target
target
make -k PRED=1eriA PRED2=1e joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1eriA/T0120-1eriA-local.pw.a2m.gz 1eriA/1eriA-T0120-local.pw.a2m.gz \
1eriA/T0120-1eriA-2track-local.pw.a2m.gz \
1eriA/T0120-1eriA-2track-global.pw.a2m.gz \
1eriA/T0120-1eriA-vit.pw.a2m.gz 1eriA/1eriA-T0120-vit.pw.a2m.gz \
1eriA/T0120-1eriA-global.pw.a2m.gz 	1eriA/1eriA-T0120-global.pw.a2m.gz \
1eriA/1eriA-T0120-fssp-global.pw.a2m.gz \
1eriA/xxxx-1eriA-T0120-local.pw.a2m.gz 1eriA/xxxx-1eriA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1eriA/T0120-1eriA-local.pw.a2m.gz' is up to date.
make[2]: `1eriA/1eriA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1eriA/T0120-1eriA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1eriA/T0120-1eriA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1eriA/T0120-1eriA-vit.pw.a2m.gz' is up to date.
make[2]: `1eriA/1eriA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1eriA/T0120-1eriA-global.pw.a2m.gz' is up to date.
make[2]: `1eriA/1eriA-T0120-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1eriA/struct-align/1eriA.fssp-w0.5.mod', needed by `1eriA/1eriA-T0120-fssp-global.pw.a2m.gz'.
make[2]: Target `1eriA/1eriA-T0120-fssp-global.pw.a2m.gz' not remade because of errors.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eriA/xxxx-1eriA-T0120-local.pw.a2m.gz'.
make[2]: Target `1eriA/xxxx-1eriA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1eriA/xxxx-1eriA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1ckqA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1ckqA/T0120-1ckqA-local.pw.a2m.gz 1ckqA/1ckqA-T0120-local.pw.a2m.gz \
1ckqA/T0120-1ckqA-2track-local.pw.a2m.gz \
1ckqA/T0120-1ckqA-2track-global.pw.a2m.gz \
1ckqA/T0120-1ckqA-vit.pw.a2m.gz 1ckqA/1ckqA-T0120-vit.pw.a2m.gz \
1ckqA/T0120-1ckqA-global.pw.a2m.gz 	1ckqA/1ckqA-T0120-global.pw.a2m.gz \
1ckqA/1ckqA-T0120-fssp-global.pw.a2m.gz \
1ckqA/xxxx-1ckqA-T0120-local.pw.a2m.gz 1ckqA/xxxx-1ckqA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1ckqA/T0120-1ckqA-local.pw.a2m.gz' is up to date.
make[2]: `1ckqA/1ckqA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1ckqA/T0120-1ckqA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1ckqA/T0120-1ckqA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1ckqA/T0120-1ckqA-vit.pw.a2m.gz' is up to date.
make[2]: `1ckqA/1ckqA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1ckqA/T0120-1ckqA-global.pw.a2m.gz' is up to date.
make[2]: `1ckqA/1ckqA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1ckqA/1ckqA-T0120-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-local.pw.a2m.gz'.
make[2]: Target `1ckqA/xxxx-1ckqA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1ckqA/xxxx-1ckqA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo remote
remote
make -k PRED=1mup  PRED2=1m joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1mup/T0120-1mup-local.pw.a2m.gz 1mup/1mup-T0120-local.pw.a2m.gz \
1mup/T0120-1mup-2track-local.pw.a2m.gz \
1mup/T0120-1mup-2track-global.pw.a2m.gz \
1mup/T0120-1mup-vit.pw.a2m.gz 1mup/1mup-T0120-vit.pw.a2m.gz \
1mup/T0120-1mup-global.pw.a2m.gz 	1mup/1mup-T0120-global.pw.a2m.gz \
1mup/1mup-T0120-fssp-global.pw.a2m.gz \
1mup/xxxx-1mup-T0120-local.pw.a2m.gz 1mup/xxxx-1mup-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1mup/T0120-1mup-local.pw.a2m.gz' is up to date.
make[2]: `1mup/1mup-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1mup/T0120-1mup-2track-local.pw.a2m.gz' is up to date.
make[2]: `1mup/T0120-1mup-2track-global.pw.a2m.gz' is up to date.
make[2]: `1mup/T0120-1mup-vit.pw.a2m.gz' is up to date.
make[2]: `1mup/1mup-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1mup/T0120-1mup-global.pw.a2m.gz' is up to date.
make[2]: `1mup/1mup-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1mup/1mup-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1mup/xxxx-1mup-T0120-local.pw.a2m.gz'.
make[2]: Target `1mup/xxxx-1mup-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1mup/xxxx-1mup-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1nsj  PRED2=1n joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1nsj/T0120-1nsj-local.pw.a2m.gz 1nsj/1nsj-T0120-local.pw.a2m.gz \
1nsj/T0120-1nsj-2track-local.pw.a2m.gz \
1nsj/T0120-1nsj-2track-global.pw.a2m.gz \
1nsj/T0120-1nsj-vit.pw.a2m.gz 1nsj/1nsj-T0120-vit.pw.a2m.gz \
1nsj/T0120-1nsj-global.pw.a2m.gz 	1nsj/1nsj-T0120-global.pw.a2m.gz \
1nsj/1nsj-T0120-fssp-global.pw.a2m.gz \
1nsj/xxxx-1nsj-T0120-local.pw.a2m.gz 1nsj/xxxx-1nsj-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1nsj/T0120-1nsj-local.pw.a2m.gz' is up to date.
make[2]: `1nsj/1nsj-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1nsj/T0120-1nsj-2track-local.pw.a2m.gz' is up to date.
make[2]: `1nsj/T0120-1nsj-2track-global.pw.a2m.gz' is up to date.
make[2]: `1nsj/T0120-1nsj-vit.pw.a2m.gz' is up to date.
make[2]: `1nsj/1nsj-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1nsj/T0120-1nsj-global.pw.a2m.gz' is up to date.
make[2]: `1nsj/1nsj-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1nsj/1nsj-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nsj/xxxx-1nsj-T0120-local.pw.a2m.gz'.
make[2]: Target `1nsj/xxxx-1nsj-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1nsj/xxxx-1nsj-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo 2track
2track
make -k PRED=1be3B PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1be3B/T0120-1be3B-local.pw.a2m.gz 1be3B/1be3B-T0120-local.pw.a2m.gz \
1be3B/T0120-1be3B-2track-local.pw.a2m.gz \
1be3B/T0120-1be3B-2track-global.pw.a2m.gz \
1be3B/T0120-1be3B-vit.pw.a2m.gz 1be3B/1be3B-T0120-vit.pw.a2m.gz \
1be3B/T0120-1be3B-global.pw.a2m.gz 	1be3B/1be3B-T0120-global.pw.a2m.gz \
1be3B/1be3B-T0120-fssp-global.pw.a2m.gz \
1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz 1be3B/xxxx-1be3B-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1be3B/T0120-1be3B-local.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-2track-local.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-2track-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-vit.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz'.
make[2]: Target `1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1be3B/xxxx-1be3B-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1atlA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1atlA/T0120-1atlA-local.pw.a2m.gz 1atlA/1atlA-T0120-local.pw.a2m.gz \
1atlA/T0120-1atlA-2track-local.pw.a2m.gz \
1atlA/T0120-1atlA-2track-global.pw.a2m.gz \
1atlA/T0120-1atlA-vit.pw.a2m.gz 1atlA/1atlA-T0120-vit.pw.a2m.gz \
1atlA/T0120-1atlA-global.pw.a2m.gz 	1atlA/1atlA-T0120-global.pw.a2m.gz \
1atlA/1atlA-T0120-fssp-global.pw.a2m.gz \
1atlA/xxxx-1atlA-T0120-local.pw.a2m.gz 1atlA/xxxx-1atlA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1atlA/T0120-1atlA-local.pw.a2m.gz' is up to date.
make[2]: `1atlA/1atlA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1atlA/T0120-1atlA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1atlA/T0120-1atlA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1atlA/T0120-1atlA-vit.pw.a2m.gz' is up to date.
make[2]: `1atlA/1atlA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1atlA/T0120-1atlA-global.pw.a2m.gz' is up to date.
make[2]: `1atlA/1atlA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1atlA/1atlA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1atlA/xxxx-1atlA-T0120-local.pw.a2m.gz'.
make[2]: Target `1atlA/xxxx-1atlA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1atlA/xxxx-1atlA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1b3qA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1b3qA/T0120-1b3qA-local.pw.a2m.gz 1b3qA/1b3qA-T0120-local.pw.a2m.gz \
1b3qA/T0120-1b3qA-2track-local.pw.a2m.gz \
1b3qA/T0120-1b3qA-2track-global.pw.a2m.gz \
1b3qA/T0120-1b3qA-vit.pw.a2m.gz 1b3qA/1b3qA-T0120-vit.pw.a2m.gz \
1b3qA/T0120-1b3qA-global.pw.a2m.gz 	1b3qA/1b3qA-T0120-global.pw.a2m.gz \
1b3qA/1b3qA-T0120-fssp-global.pw.a2m.gz \
1b3qA/xxxx-1b3qA-T0120-local.pw.a2m.gz 1b3qA/xxxx-1b3qA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1b3qA/T0120-1b3qA-local.pw.a2m.gz' is up to date.
make[2]: `1b3qA/1b3qA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1b3qA/T0120-1b3qA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1b3qA/T0120-1b3qA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1b3qA/T0120-1b3qA-vit.pw.a2m.gz' is up to date.
make[2]: `1b3qA/1b3qA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1b3qA/T0120-1b3qA-global.pw.a2m.gz' is up to date.
make[2]: `1b3qA/1b3qA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1b3qA/1b3qA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b3qA/xxxx-1b3qA-T0120-local.pw.a2m.gz'.
make[2]: Target `1b3qA/xxxx-1b3qA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1b3qA/xxxx-1b3qA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1nfp  PRED2=1n joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1nfp/T0120-1nfp-local.pw.a2m.gz 1nfp/1nfp-T0120-local.pw.a2m.gz \
1nfp/T0120-1nfp-2track-local.pw.a2m.gz \
1nfp/T0120-1nfp-2track-global.pw.a2m.gz \
1nfp/T0120-1nfp-vit.pw.a2m.gz 1nfp/1nfp-T0120-vit.pw.a2m.gz \
1nfp/T0120-1nfp-global.pw.a2m.gz 	1nfp/1nfp-T0120-global.pw.a2m.gz \
1nfp/1nfp-T0120-fssp-global.pw.a2m.gz \
1nfp/xxxx-1nfp-T0120-local.pw.a2m.gz 1nfp/xxxx-1nfp-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1nfp/T0120-1nfp-local.pw.a2m.gz' is up to date.
make[2]: `1nfp/1nfp-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1nfp/T0120-1nfp-2track-local.pw.a2m.gz' is up to date.
make[2]: `1nfp/T0120-1nfp-2track-global.pw.a2m.gz' is up to date.
make[2]: `1nfp/T0120-1nfp-vit.pw.a2m.gz' is up to date.
make[2]: `1nfp/1nfp-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1nfp/T0120-1nfp-global.pw.a2m.gz' is up to date.
make[2]: `1nfp/1nfp-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1nfp/1nfp-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nfp/xxxx-1nfp-T0120-local.pw.a2m.gz'.
make[2]: Target `1nfp/xxxx-1nfp-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1nfp/xxxx-1nfp-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1ltm  PRED2=1l joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1ltm/T0120-1ltm-local.pw.a2m.gz 1ltm/1ltm-T0120-local.pw.a2m.gz \
1ltm/T0120-1ltm-2track-local.pw.a2m.gz \
1ltm/T0120-1ltm-2track-global.pw.a2m.gz \
1ltm/T0120-1ltm-vit.pw.a2m.gz 1ltm/1ltm-T0120-vit.pw.a2m.gz \
1ltm/T0120-1ltm-global.pw.a2m.gz 	1ltm/1ltm-T0120-global.pw.a2m.gz \
1ltm/1ltm-T0120-fssp-global.pw.a2m.gz \
1ltm/xxxx-1ltm-T0120-local.pw.a2m.gz 1ltm/xxxx-1ltm-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1ltm/T0120-1ltm-local.pw.a2m.gz' is up to date.
make[2]: `1ltm/1ltm-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1ltm/T0120-1ltm-2track-local.pw.a2m.gz' is up to date.
make[2]: `1ltm/T0120-1ltm-2track-global.pw.a2m.gz' is up to date.
make[2]: `1ltm/T0120-1ltm-vit.pw.a2m.gz' is up to date.
make[2]: `1ltm/1ltm-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1ltm/T0120-1ltm-global.pw.a2m.gz' is up to date.
make[2]: `1ltm/1ltm-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1ltm/1ltm-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ltm/xxxx-1ltm-T0120-local.pw.a2m.gz'.
make[2]: Target `1ltm/xxxx-1ltm-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1ltm/xxxx-1ltm-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1c4xA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1c4xA/T0120-1c4xA-local.pw.a2m.gz 1c4xA/1c4xA-T0120-local.pw.a2m.gz \
1c4xA/T0120-1c4xA-2track-local.pw.a2m.gz \
1c4xA/T0120-1c4xA-2track-global.pw.a2m.gz \
1c4xA/T0120-1c4xA-vit.pw.a2m.gz 1c4xA/1c4xA-T0120-vit.pw.a2m.gz \
1c4xA/T0120-1c4xA-global.pw.a2m.gz 	1c4xA/1c4xA-T0120-global.pw.a2m.gz \
1c4xA/1c4xA-T0120-fssp-global.pw.a2m.gz \
1c4xA/xxxx-1c4xA-T0120-local.pw.a2m.gz 1c4xA/xxxx-1c4xA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1c4xA/T0120-1c4xA-local.pw.a2m.gz' is up to date.
make[2]: `1c4xA/1c4xA-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1c4xA/T0120-1c4xA-2track-local.pw.a2m.gz' is up to date.
make[2]: `1c4xA/T0120-1c4xA-2track-global.pw.a2m.gz' is up to date.
make[2]: `1c4xA/T0120-1c4xA-vit.pw.a2m.gz' is up to date.
make[2]: `1c4xA/1c4xA-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1c4xA/T0120-1c4xA-global.pw.a2m.gz' is up to date.
make[2]: `1c4xA/1c4xA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1c4xA/1c4xA-T0120-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-local.pw.a2m.gz'.
make[2]: Target `1c4xA/xxxx-1c4xA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1c4xA/xxxx-1c4xA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo template
template
make -k PRED=1quuA PRED2=1q A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1quuA/T0120-1quuA-local.pw.a2m.gz 1quuA/1quuA-T0120-local.pw.a2m.gz \
1quuA/T0120-1quuA-2track-local.pw.a2m.gz \
1quuA/T0120-1quuA-2track-global.pw.a2m.gz \
1quuA/T0120-1quuA-vit.pw.a2m.gz 1quuA/1quuA-T0120-vit.pw.a2m.gz \
1quuA/T0120-1quuA-global.pw.a2m.gz 	1quuA/1quuA-T0120-global.pw.a2m.gz \
1quuA/1quuA-T0120-fssp-global.pw.a2m.gz \
1quuA/xxxx-1quuA-T0120-local.pw.a2m.gz 1quuA/xxxx-1quuA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1quuA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1quuA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0120-1quuA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.528000
Database has 3 sequences with 834 residues.
gzip -f 1quuA/T0120-1quuA-local.pw.a2m
make[2]: `1quuA/1quuA-T0120-local.pw.a2m.gz' is up to date.
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0120.remote-t2k.2d.rdb T0120.remote-t2k-2d.mod
make 1quuA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1quuA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0120-1quuA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -121.694000
Database has 3 sequences with 834 residues.
gzip -f 1quuA/T0120-1quuA-2track-local.pw.a2m
make 1quuA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1quuA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0120-1quuA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -104.280327
Database has 3 sequences with 834 residues.
gzip -f 1quuA/T0120-1quuA-2track-global.pw.a2m
make 1quuA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1quuA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0120-1quuA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.369995
Database has 3 sequences with 834 residues.
gzip -f 1quuA/T0120-1quuA-vit.pw.a2m
make[2]: `1quuA/1quuA-T0120-vit.pw.a2m.gz' is up to date.
make 1quuA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1quuA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1quuA/T0120-1quuA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1quuA/info/1quuA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -130.040329
Database has 3 sequences with 834 residues.
gzip -f 1quuA/T0120-1quuA-global.pw.a2m
make[2]: `1quuA/1quuA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1quuA/1quuA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1quuA/xxxx-1quuA-T0120-local.pw.a2m.gz'.
make[2]: Target `1quuA/xxxx-1quuA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1quuA/xxxx-1quuA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1kvs  PRED2=1k A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1kvs/T0120-1kvs-local.pw.a2m.gz 1kvs/1kvs-T0120-local.pw.a2m.gz \
1kvs/T0120-1kvs-2track-local.pw.a2m.gz \
1kvs/T0120-1kvs-2track-global.pw.a2m.gz \
1kvs/T0120-1kvs-vit.pw.a2m.gz 1kvs/1kvs-T0120-vit.pw.a2m.gz \
1kvs/T0120-1kvs-global.pw.a2m.gz 	1kvs/1kvs-T0120-global.pw.a2m.gz \
1kvs/1kvs-T0120-fssp-global.pw.a2m.gz \
1kvs/xxxx-1kvs-T0120-local.pw.a2m.gz 1kvs/xxxx-1kvs-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1kvs
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1kvs' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1kvs/T0120-1kvs-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.379929
Database has 3 sequences with 1012 residues.
gzip -f 1kvs/T0120-1kvs-local.pw.a2m
make[2]: `1kvs/1kvs-T0120-local.pw.a2m.gz' is up to date.
make 1kvs
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1kvs' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1kvs/T0120-1kvs-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -118.092094
Database has 3 sequences with 1012 residues.
gzip -f 1kvs/T0120-1kvs-2track-local.pw.a2m
make 1kvs
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1kvs' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1kvs/T0120-1kvs-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -97.928162
Database has 3 sequences with 1012 residues.
gzip -f 1kvs/T0120-1kvs-2track-global.pw.a2m
make 1kvs
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1kvs' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1kvs/T0120-1kvs-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.468933
Database has 3 sequences with 1012 residues.
gzip -f 1kvs/T0120-1kvs-vit.pw.a2m
make[2]: `1kvs/1kvs-T0120-vit.pw.a2m.gz' is up to date.
make 1kvs
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1kvs' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1kvs/T0120-1kvs-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1k/1kvs/info/1kvs.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -125.878349
Database has 3 sequences with 1012 residues.
gzip -f 1kvs/T0120-1kvs-global.pw.a2m
make[2]: `1kvs/1kvs-T0120-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kvs/struct-align/1kvs.fssp-w0.5.mod', needed by `1kvs/1kvs-T0120-fssp-global.pw.a2m.gz'.
make[2]: Target `1kvs/1kvs-T0120-fssp-global.pw.a2m.gz' not remade because of errors.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kvs/xxxx-1kvs-T0120-local.pw.a2m.gz'.
make[2]: Target `1kvs/xxxx-1kvs-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1kvs/xxxx-1kvs-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1c8zA PRED2=1c A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1c8zA/T0120-1c8zA-local.pw.a2m.gz 1c8zA/1c8zA-T0120-local.pw.a2m.gz \
1c8zA/T0120-1c8zA-2track-local.pw.a2m.gz \
1c8zA/T0120-1c8zA-2track-global.pw.a2m.gz \
1c8zA/T0120-1c8zA-vit.pw.a2m.gz 1c8zA/1c8zA-T0120-vit.pw.a2m.gz \
1c8zA/T0120-1c8zA-global.pw.a2m.gz 	1c8zA/1c8zA-T0120-global.pw.a2m.gz \
1c8zA/1c8zA-T0120-fssp-global.pw.a2m.gz \
1c8zA/xxxx-1c8zA-T0120-local.pw.a2m.gz 1c8zA/xxxx-1c8zA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1c8zA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c8zA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c8zA/T0120-1c8zA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -146.025467
Database has 3 sequences with 866 residues.
gzip -f 1c8zA/T0120-1c8zA-local.pw.a2m
make[2]: `1c8zA/1c8zA-T0120-local.pw.a2m.gz' is up to date.
make 1c8zA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c8zA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c8zA/T0120-1c8zA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -115.711975
Database has 3 sequences with 866 residues.
gzip -f 1c8zA/T0120-1c8zA-2track-local.pw.a2m
make 1c8zA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c8zA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c8zA/T0120-1c8zA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -92.308510
Database has 3 sequences with 866 residues.
gzip -f 1c8zA/T0120-1c8zA-2track-global.pw.a2m
make 1c8zA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c8zA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c8zA/T0120-1c8zA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.865784
Database has 3 sequences with 866 residues.
gzip -f 1c8zA/T0120-1c8zA-vit.pw.a2m
make[2]: `1c8zA/1c8zA-T0120-vit.pw.a2m.gz' is up to date.
make 1c8zA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c8zA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c8zA/T0120-1c8zA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c8zA/info/1c8zA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -132.601013
Database has 3 sequences with 866 residues.
gzip -f 1c8zA/T0120-1c8zA-global.pw.a2m
make[2]: `1c8zA/1c8zA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1c8zA/1c8zA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c8zA/xxxx-1c8zA-T0120-local.pw.a2m.gz'.
make[2]: Target `1c8zA/xxxx-1c8zA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1c8zA/xxxx-1c8zA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo target
target
make -k PRED=1eriA PRED2=1e A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1eriA/T0120-1eriA-local.pw.a2m.gz 1eriA/1eriA-T0120-local.pw.a2m.gz \
1eriA/T0120-1eriA-2track-local.pw.a2m.gz \
1eriA/T0120-1eriA-2track-global.pw.a2m.gz \
1eriA/T0120-1eriA-vit.pw.a2m.gz 1eriA/1eriA-T0120-vit.pw.a2m.gz \
1eriA/T0120-1eriA-global.pw.a2m.gz 	1eriA/1eriA-T0120-global.pw.a2m.gz \
1eriA/1eriA-T0120-fssp-global.pw.a2m.gz \
1eriA/xxxx-1eriA-T0120-local.pw.a2m.gz 1eriA/xxxx-1eriA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1eriA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1eriA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1eriA/T0120-1eriA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.604309
Database has 3 sequences with 873 residues.
gzip -f 1eriA/T0120-1eriA-local.pw.a2m
make[2]: `1eriA/1eriA-T0120-local.pw.a2m.gz' is up to date.
make 1eriA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1eriA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1eriA/T0120-1eriA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -115.898651
Database has 3 sequences with 873 residues.
gzip -f 1eriA/T0120-1eriA-2track-local.pw.a2m
make 1eriA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1eriA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1eriA/T0120-1eriA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.687996
Database has 3 sequences with 873 residues.
gzip -f 1eriA/T0120-1eriA-2track-global.pw.a2m
make 1eriA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1eriA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1eriA/T0120-1eriA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.144653
Database has 3 sequences with 873 residues.
gzip -f 1eriA/T0120-1eriA-vit.pw.a2m
make[2]: `1eriA/1eriA-T0120-vit.pw.a2m.gz' is up to date.
make 1eriA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1eriA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1eriA/T0120-1eriA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1e/1eriA/info/1eriA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -129.475327
Database has 3 sequences with 873 residues.
gzip -f 1eriA/T0120-1eriA-global.pw.a2m
make[2]: `1eriA/1eriA-T0120-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1eriA/struct-align/1eriA.fssp-w0.5.mod', needed by `1eriA/1eriA-T0120-fssp-global.pw.a2m.gz'.
make[2]: Target `1eriA/1eriA-T0120-fssp-global.pw.a2m.gz' not remade because of errors.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eriA/xxxx-1eriA-T0120-local.pw.a2m.gz'.
make[2]: Target `1eriA/xxxx-1eriA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1eriA/xxxx-1eriA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1ckqA PRED2=1c A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1ckqA/T0120-1ckqA-local.pw.a2m.gz 1ckqA/1ckqA-T0120-local.pw.a2m.gz \
1ckqA/T0120-1ckqA-2track-local.pw.a2m.gz \
1ckqA/T0120-1ckqA-2track-global.pw.a2m.gz \
1ckqA/T0120-1ckqA-vit.pw.a2m.gz 1ckqA/1ckqA-T0120-vit.pw.a2m.gz \
1ckqA/T0120-1ckqA-global.pw.a2m.gz 	1ckqA/1ckqA-T0120-global.pw.a2m.gz \
1ckqA/1ckqA-T0120-fssp-global.pw.a2m.gz \
1ckqA/xxxx-1ckqA-T0120-local.pw.a2m.gz 1ckqA/xxxx-1ckqA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1ckqA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ckqA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ckqA/T0120-1ckqA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.604309
Database has 3 sequences with 873 residues.
gzip -f 1ckqA/T0120-1ckqA-local.pw.a2m
make[2]: `1ckqA/1ckqA-T0120-local.pw.a2m.gz' is up to date.
make 1ckqA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ckqA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ckqA/T0120-1ckqA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -115.593323
Database has 3 sequences with 873 residues.
gzip -f 1ckqA/T0120-1ckqA-2track-local.pw.a2m
make 1ckqA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ckqA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ckqA/T0120-1ckqA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -100.999329
Database has 3 sequences with 873 residues.
gzip -f 1ckqA/T0120-1ckqA-2track-global.pw.a2m
make 1ckqA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ckqA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ckqA/T0120-1ckqA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.144653
Database has 3 sequences with 873 residues.
gzip -f 1ckqA/T0120-1ckqA-vit.pw.a2m
make[2]: `1ckqA/1ckqA-T0120-vit.pw.a2m.gz' is up to date.
make 1ckqA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ckqA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ckqA/T0120-1ckqA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1ckqA/info/1ckqA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -129.475327
Database has 3 sequences with 873 residues.
gzip -f 1ckqA/T0120-1ckqA-global.pw.a2m
make[2]: `1ckqA/1ckqA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1ckqA/1ckqA-T0120-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-local.pw.a2m.gz'.
make[2]: Target `1ckqA/xxxx-1ckqA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1ckqA/xxxx-1ckqA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo remote
remote
make -k PRED=1mup  PRED2=1m A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1mup/T0120-1mup-local.pw.a2m.gz 1mup/1mup-T0120-local.pw.a2m.gz \
1mup/T0120-1mup-2track-local.pw.a2m.gz \
1mup/T0120-1mup-2track-global.pw.a2m.gz \
1mup/T0120-1mup-vit.pw.a2m.gz 1mup/1mup-T0120-vit.pw.a2m.gz \
1mup/T0120-1mup-global.pw.a2m.gz 	1mup/1mup-T0120-global.pw.a2m.gz \
1mup/1mup-T0120-fssp-global.pw.a2m.gz \
1mup/xxxx-1mup-T0120-local.pw.a2m.gz 1mup/xxxx-1mup-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1mup
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1mup' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1mup/T0120-1mup-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -150.936890
Database has 3 sequences with 659 residues.
gzip -f 1mup/T0120-1mup-local.pw.a2m
make[2]: `1mup/1mup-T0120-local.pw.a2m.gz' is up to date.
make 1mup
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1mup' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1mup/T0120-1mup-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride.seq,/projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -119.163216
Database has 3 sequences with 659 residues.
gzip -f 1mup/T0120-1mup-2track-local.pw.a2m
make 1mup
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1mup' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1mup/T0120-1mup-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride.seq,/projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.672325
Database has 3 sequences with 659 residues.
gzip -f 1mup/T0120-1mup-2track-global.pw.a2m
make 1mup
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1mup' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1mup/T0120-1mup-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.652206
Database has 3 sequences with 659 residues.
gzip -f 1mup/T0120-1mup-vit.pw.a2m
make[2]: `1mup/1mup-T0120-vit.pw.a2m.gz' is up to date.
make 1mup
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1mup' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1mup/T0120-1mup-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1m/1mup/info/1mup.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -142.114334
Database has 3 sequences with 659 residues.
gzip -f 1mup/T0120-1mup-global.pw.a2m
make[2]: `1mup/1mup-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1mup/1mup-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1mup/xxxx-1mup-T0120-local.pw.a2m.gz'.
make[2]: Target `1mup/xxxx-1mup-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1mup/xxxx-1mup-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1nsj  PRED2=1n A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1nsj/T0120-1nsj-local.pw.a2m.gz 1nsj/1nsj-T0120-local.pw.a2m.gz \
1nsj/T0120-1nsj-2track-local.pw.a2m.gz \
1nsj/T0120-1nsj-2track-global.pw.a2m.gz \
1nsj/T0120-1nsj-vit.pw.a2m.gz 1nsj/1nsj-T0120-vit.pw.a2m.gz \
1nsj/T0120-1nsj-global.pw.a2m.gz 	1nsj/1nsj-T0120-global.pw.a2m.gz \
1nsj/1nsj-T0120-fssp-global.pw.a2m.gz \
1nsj/xxxx-1nsj-T0120-local.pw.a2m.gz 1nsj/xxxx-1nsj-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1nsj
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nsj' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nsj/T0120-1nsj-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -151.492645
Database has 3 sequences with 746 residues.
gzip -f 1nsj/T0120-1nsj-local.pw.a2m
make[2]: `1nsj/1nsj-T0120-local.pw.a2m.gz' is up to date.
make 1nsj
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nsj' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nsj/T0120-1nsj-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -112.528114
Database has 3 sequences with 746 residues.
gzip -f 1nsj/T0120-1nsj-2track-local.pw.a2m
make 1nsj
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nsj' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nsj/T0120-1nsj-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -102.089500
Database has 3 sequences with 746 residues.
gzip -f 1nsj/T0120-1nsj-2track-global.pw.a2m
make 1nsj
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nsj' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nsj/T0120-1nsj-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -146.695633
Database has 3 sequences with 746 residues.
gzip -f 1nsj/T0120-1nsj-vit.pw.a2m
make[2]: `1nsj/1nsj-T0120-vit.pw.a2m.gz' is up to date.
make 1nsj
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nsj' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nsj/T0120-1nsj-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nsj/info/1nsj.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -146.983673
Database has 3 sequences with 746 residues.
gzip -f 1nsj/T0120-1nsj-global.pw.a2m
make[2]: `1nsj/1nsj-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1nsj/1nsj-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nsj/xxxx-1nsj-T0120-local.pw.a2m.gz'.
make[2]: Target `1nsj/xxxx-1nsj-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1nsj/xxxx-1nsj-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo 2track
2track
make -k PRED=1be3B PRED2=1b A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1be3B/T0120-1be3B-local.pw.a2m.gz 1be3B/1be3B-T0120-local.pw.a2m.gz \
1be3B/T0120-1be3B-2track-local.pw.a2m.gz \
1be3B/T0120-1be3B-2track-global.pw.a2m.gz \
1be3B/T0120-1be3B-vit.pw.a2m.gz 1be3B/1be3B-T0120-vit.pw.a2m.gz \
1be3B/T0120-1be3B-global.pw.a2m.gz 	1be3B/1be3B-T0120-global.pw.a2m.gz \
1be3B/1be3B-T0120-fssp-global.pw.a2m.gz \
1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz 1be3B/xxxx-1be3B-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1be3B
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1be3B' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1be3B/T0120-1be3B-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.464874
Database has 3 sequences with 1194 residues.
gzip -f 1be3B/T0120-1be3B-local.pw.a2m
make[2]: `1be3B/1be3B-T0120-local.pw.a2m.gz' is up to date.
make 1be3B
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1be3B' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1be3B/T0120-1be3B-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -119.898338
Database has 3 sequences with 1194 residues.
gzip -f 1be3B/T0120-1be3B-2track-local.pw.a2m
make 1be3B
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1be3B' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1be3B/T0120-1be3B-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -84.104820
Database has 3 sequences with 1194 residues.
gzip -f 1be3B/T0120-1be3B-2track-global.pw.a2m
make 1be3B
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1be3B' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1be3B/T0120-1be3B-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.902161
Database has 3 sequences with 1194 residues.
gzip -f 1be3B/T0120-1be3B-vit.pw.a2m
make[2]: `1be3B/1be3B-T0120-vit.pw.a2m.gz' is up to date.
make 1be3B
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1be3B' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1be3B/T0120-1be3B-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1be3B/info/1be3B.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -114.842674
Database has 3 sequences with 1194 residues.
gzip -f 1be3B/T0120-1be3B-global.pw.a2m
make[2]: `1be3B/1be3B-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz'.
make[2]: Target `1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1be3B/xxxx-1be3B-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1atlA PRED2=1a A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1atlA/T0120-1atlA-local.pw.a2m.gz 1atlA/1atlA-T0120-local.pw.a2m.gz \
1atlA/T0120-1atlA-2track-local.pw.a2m.gz \
1atlA/T0120-1atlA-2track-global.pw.a2m.gz \
1atlA/T0120-1atlA-vit.pw.a2m.gz 1atlA/1atlA-T0120-vit.pw.a2m.gz \
1atlA/T0120-1atlA-global.pw.a2m.gz 	1atlA/1atlA-T0120-global.pw.a2m.gz \
1atlA/1atlA-T0120-fssp-global.pw.a2m.gz \
1atlA/xxxx-1atlA-T0120-local.pw.a2m.gz 1atlA/xxxx-1atlA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1atlA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1atlA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1atlA/T0120-1atlA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.223434
Database has 3 sequences with 738 residues.
gzip -f 1atlA/T0120-1atlA-local.pw.a2m
make[2]: `1atlA/1atlA-T0120-local.pw.a2m.gz' is up to date.
make 1atlA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1atlA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1atlA/T0120-1atlA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -113.030266
Database has 3 sequences with 738 residues.
gzip -f 1atlA/T0120-1atlA-2track-local.pw.a2m
make 1atlA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1atlA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1atlA/T0120-1atlA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -105.410492
Database has 3 sequences with 738 residues.
gzip -f 1atlA/T0120-1atlA-2track-global.pw.a2m
make 1atlA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1atlA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1atlA/T0120-1atlA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.578094
Database has 3 sequences with 738 residues.
gzip -f 1atlA/T0120-1atlA-vit.pw.a2m
make[2]: `1atlA/1atlA-T0120-vit.pw.a2m.gz' is up to date.
make 1atlA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1atlA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1atlA/T0120-1atlA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1atlA/info/1atlA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -136.700333
Database has 3 sequences with 738 residues.
gzip -f 1atlA/T0120-1atlA-global.pw.a2m
make[2]: `1atlA/1atlA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1atlA/1atlA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1atlA/xxxx-1atlA-T0120-local.pw.a2m.gz'.
make[2]: Target `1atlA/xxxx-1atlA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1atlA/xxxx-1atlA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1b3qA PRED2=1b A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1b3qA/T0120-1b3qA-local.pw.a2m.gz 1b3qA/1b3qA-T0120-local.pw.a2m.gz \
1b3qA/T0120-1b3qA-2track-local.pw.a2m.gz \
1b3qA/T0120-1b3qA-2track-global.pw.a2m.gz \
1b3qA/T0120-1b3qA-vit.pw.a2m.gz 1b3qA/1b3qA-T0120-vit.pw.a2m.gz \
1b3qA/T0120-1b3qA-global.pw.a2m.gz 	1b3qA/1b3qA-T0120-global.pw.a2m.gz \
1b3qA/1b3qA-T0120-fssp-global.pw.a2m.gz \
1b3qA/xxxx-1b3qA-T0120-local.pw.a2m.gz 1b3qA/xxxx-1b3qA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1b3qA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1b3qA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1b3qA/T0120-1b3qA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -146.087769
Database has 3 sequences with 1083 residues.
gzip -f 1b3qA/T0120-1b3qA-local.pw.a2m
make[2]: `1b3qA/1b3qA-T0120-local.pw.a2m.gz' is up to date.
make 1b3qA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1b3qA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1b3qA/T0120-1b3qA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -115.452423
Database has 3 sequences with 1083 residues.
gzip -f 1b3qA/T0120-1b3qA-2track-local.pw.a2m
make 1b3qA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1b3qA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1b3qA/T0120-1b3qA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -83.393669
Database has 3 sequences with 1083 residues.
gzip -f 1b3qA/T0120-1b3qA-2track-global.pw.a2m
make 1b3qA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1b3qA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1b3qA/T0120-1b3qA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.946106
Database has 3 sequences with 1083 residues.
gzip -f 1b3qA/T0120-1b3qA-vit.pw.a2m
make[2]: `1b3qA/1b3qA-T0120-vit.pw.a2m.gz' is up to date.
make 1b3qA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1b3qA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1b3qA/T0120-1b3qA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b3qA/info/1b3qA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -123.415344
Database has 3 sequences with 1083 residues.
gzip -f 1b3qA/T0120-1b3qA-global.pw.a2m
make[2]: `1b3qA/1b3qA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1b3qA/1b3qA-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b3qA/xxxx-1b3qA-T0120-local.pw.a2m.gz'.
make[2]: Target `1b3qA/xxxx-1b3qA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1b3qA/xxxx-1b3qA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1nfp  PRED2=1n A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1nfp/T0120-1nfp-local.pw.a2m.gz 1nfp/1nfp-T0120-local.pw.a2m.gz \
1nfp/T0120-1nfp-2track-local.pw.a2m.gz \
1nfp/T0120-1nfp-2track-global.pw.a2m.gz \
1nfp/T0120-1nfp-vit.pw.a2m.gz 1nfp/1nfp-T0120-vit.pw.a2m.gz \
1nfp/T0120-1nfp-global.pw.a2m.gz 	1nfp/1nfp-T0120-global.pw.a2m.gz \
1nfp/1nfp-T0120-fssp-global.pw.a2m.gz \
1nfp/xxxx-1nfp-T0120-local.pw.a2m.gz 1nfp/xxxx-1nfp-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1nfp
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nfp' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nfp/T0120-1nfp-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.445724
Database has 3 sequences with 792 residues.
gzip -f 1nfp/T0120-1nfp-local.pw.a2m
make[2]: `1nfp/1nfp-T0120-local.pw.a2m.gz' is up to date.
make 1nfp
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nfp' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nfp/T0120-1nfp-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -116.619225
Database has 3 sequences with 792 residues.
gzip -f 1nfp/T0120-1nfp-2track-local.pw.a2m
make 1nfp
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nfp' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nfp/T0120-1nfp-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -108.065498
Database has 3 sequences with 792 residues.
gzip -f 1nfp/T0120-1nfp-2track-global.pw.a2m
make 1nfp
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nfp' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nfp/T0120-1nfp-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -142.415390
Database has 3 sequences with 792 residues.
gzip -f 1nfp/T0120-1nfp-vit.pw.a2m
make[2]: `1nfp/1nfp-T0120-vit.pw.a2m.gz' is up to date.
make 1nfp
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1nfp' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1nfp/T0120-1nfp-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nfp/info/1nfp.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -133.219009
Database has 3 sequences with 792 residues.
gzip -f 1nfp/T0120-1nfp-global.pw.a2m
make[2]: `1nfp/1nfp-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1nfp/1nfp-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nfp/xxxx-1nfp-T0120-local.pw.a2m.gz'.
make[2]: Target `1nfp/xxxx-1nfp-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1nfp/xxxx-1nfp-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1ltm  PRED2=1l A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1ltm/T0120-1ltm-local.pw.a2m.gz 1ltm/1ltm-T0120-local.pw.a2m.gz \
1ltm/T0120-1ltm-2track-local.pw.a2m.gz \
1ltm/T0120-1ltm-2track-global.pw.a2m.gz \
1ltm/T0120-1ltm-vit.pw.a2m.gz 1ltm/1ltm-T0120-vit.pw.a2m.gz \
1ltm/T0120-1ltm-global.pw.a2m.gz 	1ltm/1ltm-T0120-global.pw.a2m.gz \
1ltm/1ltm-T0120-fssp-global.pw.a2m.gz \
1ltm/xxxx-1ltm-T0120-local.pw.a2m.gz 1ltm/xxxx-1ltm-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1ltm
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ltm' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ltm/T0120-1ltm-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.038071
Database has 3 sequences with 965 residues.
gzip -f 1ltm/T0120-1ltm-local.pw.a2m
make[2]: `1ltm/1ltm-T0120-local.pw.a2m.gz' is up to date.
make 1ltm
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ltm' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ltm/T0120-1ltm-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -115.212563
Database has 3 sequences with 965 residues.
gzip -f 1ltm/T0120-1ltm-2track-local.pw.a2m
make 1ltm
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ltm' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ltm/T0120-1ltm-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -100.201820
Database has 3 sequences with 965 residues.
gzip -f 1ltm/T0120-1ltm-2track-global.pw.a2m
make 1ltm
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ltm' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ltm/T0120-1ltm-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -139.821060
Database has 3 sequences with 965 residues.
gzip -f 1ltm/T0120-1ltm-vit.pw.a2m
make[2]: `1ltm/1ltm-T0120-vit.pw.a2m.gz' is up to date.
make 1ltm
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1ltm' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1ltm/T0120-1ltm-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1l/1ltm/info/1ltm.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -123.316673
Database has 3 sequences with 965 residues.
gzip -f 1ltm/T0120-1ltm-global.pw.a2m
make[2]: `1ltm/1ltm-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1ltm/1ltm-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ltm/xxxx-1ltm-T0120-local.pw.a2m.gz'.
make[2]: Target `1ltm/xxxx-1ltm-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1ltm/xxxx-1ltm-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1c4xA PRED2=1c A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1c4xA/T0120-1c4xA-local.pw.a2m.gz 1c4xA/1c4xA-T0120-local.pw.a2m.gz \
1c4xA/T0120-1c4xA-2track-local.pw.a2m.gz \
1c4xA/T0120-1c4xA-2track-global.pw.a2m.gz \
1c4xA/T0120-1c4xA-vit.pw.a2m.gz 1c4xA/1c4xA-T0120-vit.pw.a2m.gz \
1c4xA/T0120-1c4xA-global.pw.a2m.gz 	1c4xA/1c4xA-T0120-global.pw.a2m.gz \
1c4xA/1c4xA-T0120-fssp-global.pw.a2m.gz \
1c4xA/xxxx-1c4xA-T0120-local.pw.a2m.gz 1c4xA/xxxx-1c4xA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1c4xA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c4xA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c4xA/T0120-1c4xA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.268005
Database has 3 sequences with 902 residues.
gzip -f 1c4xA/T0120-1c4xA-local.pw.a2m
make[2]: `1c4xA/1c4xA-T0120-local.pw.a2m.gz' is up to date.
make 1c4xA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c4xA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c4xA/T0120-1c4xA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -113.503670
Database has 3 sequences with 902 residues.
gzip -f 1c4xA/T0120-1c4xA-2track-local.pw.a2m
make 1c4xA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c4xA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c4xA/T0120-1c4xA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.765656
Database has 3 sequences with 902 residues.
gzip -f 1c4xA/T0120-1c4xA-2track-global.pw.a2m
make 1c4xA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c4xA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c4xA/T0120-1c4xA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.409332
Database has 3 sequences with 902 residues.
gzip -f 1c4xA/T0120-1c4xA-vit.pw.a2m
make[2]: `1c4xA/1c4xA-T0120-vit.pw.a2m.gz' is up to date.
make 1c4xA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c4xA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c4xA/T0120-1c4xA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c4xA/info/1c4xA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -128.916000
Database has 3 sequences with 902 residues.
gzip -f 1c4xA/T0120-1c4xA-global.pw.a2m
make[2]: `1c4xA/1c4xA-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1c4xA/1c4xA-T0120-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-local.pw.a2m.gz'.
make[2]: Target `1c4xA/xxxx-1c4xA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1c4xA/xxxx-1c4xA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
echo remote 2track
remote 2track
make -k PRED=1dceA PRED2=1d A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1dceA/T0120-1dceA-local.pw.a2m.gz 1dceA/1dceA-T0120-local.pw.a2m.gz \
1dceA/T0120-1dceA-2track-local.pw.a2m.gz \
1dceA/T0120-1dceA-2track-global.pw.a2m.gz \
1dceA/T0120-1dceA-vit.pw.a2m.gz 1dceA/1dceA-T0120-vit.pw.a2m.gz \
1dceA/T0120-1dceA-global.pw.a2m.gz 	1dceA/1dceA-T0120-global.pw.a2m.gz \
1dceA/1dceA-T0120-fssp-global.pw.a2m.gz \
1dceA/xxxx-1dceA-T0120-local.pw.a2m.gz 1dceA/xxxx-1dceA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1dceA
fixmode 1dceA
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/T0120-1dceA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -146.575165
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/T0120-1dceA-local.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/1dceA-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2481/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:        -214.351151
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/1dceA-T0120-local.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/T0120-1dceA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -123.858925
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/T0120-1dceA-2track-local.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/T0120-1dceA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -64.792473
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/T0120-1dceA-2track-global.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/T0120-1dceA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -142.846802
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/T0120-1dceA-vit.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/1dceA-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2481/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:        -209.826828
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/1dceA-T0120-vit.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/T0120-1dceA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -94.088341
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/T0120-1dceA-global.pw.a2m
make 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/1dceA-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dceA/nostruct-align/1dceA.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2481/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:        -208.641678
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/1dceA-T0120-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12473


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12473/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.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/1d/1dceA/struct-align/1dceA.fssp.a2m.gz (5 sequences, 567 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12473/tmp.a2m.
Dropping 1 (of 5) duplicate sequences with differing IDs
4 sequences left after dropping 1 of 5 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12473/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12473/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-12473/tmp.a2m (4 sequences, 567 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12473/tmp.mod /projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12473 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1dceA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dceA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dceA/1dceA-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dceA/info/1dceA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dceA/struct-align/1dceA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12473/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:        -490.260345
Database has 3 sequences with 1471 residues.
gzip -f 1dceA/1dceA-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dceA/xxxx-1dceA-T0120-local.pw.a2m.gz'.
make[2]: Target `1dceA/xxxx-1dceA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1dceA/xxxx-1dceA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1dkzA PRED2=1d A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1dkzA/T0120-1dkzA-local.pw.a2m.gz 1dkzA/1dkzA-T0120-local.pw.a2m.gz \
1dkzA/T0120-1dkzA-2track-local.pw.a2m.gz \
1dkzA/T0120-1dkzA-2track-global.pw.a2m.gz \
1dkzA/T0120-1dkzA-vit.pw.a2m.gz 1dkzA/1dkzA-T0120-vit.pw.a2m.gz \
1dkzA/T0120-1dkzA-global.pw.a2m.gz 	1dkzA/1dkzA-T0120-global.pw.a2m.gz \
1dkzA/1dkzA-T0120-fssp-global.pw.a2m.gz \
1dkzA/xxxx-1dkzA-T0120-local.pw.a2m.gz 1dkzA/xxxx-1dkzA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1dkzA
fixmode 1dkzA
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/T0120-1dkzA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.351730
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/T0120-1dkzA-local.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/1dkzA-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21094/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:        -143.597382
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/1dkzA-T0120-local.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/T0120-1dkzA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -124.320045
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/T0120-1dkzA-2track-local.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/T0120-1dkzA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -116.511322
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/T0120-1dkzA-2track-global.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/T0120-1dkzA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -142.355713
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/T0120-1dkzA-vit.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/1dkzA-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21094/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:        -139.974380
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/1dkzA-T0120-vit.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/T0120-1dkzA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -133.116333
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/T0120-1dkzA-global.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/1dkzA-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dkzA/nostruct-align/1dkzA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-21094/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:        -138.208664
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/1dkzA-T0120-global.pw.a2m
make 1dkzA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1dkzA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1dkzA/1dkzA-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dkzA/struct-align/1dkzA.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dkzA/info/1dkzA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dkzA/struct-align/1dkzA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dkzA/struct-align/1dkzA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-9718/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:        -187.007996
Database has 3 sequences with 770 residues.
gzip -f 1dkzA/1dkzA-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dkzA/xxxx-1dkzA-T0120-local.pw.a2m.gz'.
make[2]: Target `1dkzA/xxxx-1dkzA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1dkzA/xxxx-1dkzA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1a87  PRED2=1a A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1a87/T0120-1a87-local.pw.a2m.gz 1a87/1a87-T0120-local.pw.a2m.gz \
1a87/T0120-1a87-2track-local.pw.a2m.gz \
1a87/T0120-1a87-2track-global.pw.a2m.gz \
1a87/T0120-1a87-vit.pw.a2m.gz 1a87/1a87-T0120-vit.pw.a2m.gz \
1a87/T0120-1a87-global.pw.a2m.gz 	1a87/1a87-T0120-global.pw.a2m.gz \
1a87/1a87-T0120-fssp-global.pw.a2m.gz \
1a87/xxxx-1a87-T0120-local.pw.a2m.gz 1a87/xxxx-1a87-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1a87
fixmode 1a87
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/T0120-1a87-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -146.571899
Database has 3 sequences with 954 residues.
gzip -f 1a87/T0120-1a87-local.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/1a87-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30057/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:        -198.975235
Database has 3 sequences with 954 residues.
gzip -f 1a87/1a87-T0120-local.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/T0120-1a87-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -125.398743
Database has 3 sequences with 954 residues.
gzip -f 1a87/T0120-1a87-2track-local.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/T0120-1a87-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -109.229820
Database has 3 sequences with 954 residues.
gzip -f 1a87/T0120-1a87-2track-global.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/T0120-1a87-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.102554
Database has 3 sequences with 954 residues.
gzip -f 1a87/T0120-1a87-vit.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/1a87-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30057/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:        -194.918564
Database has 3 sequences with 954 residues.
gzip -f 1a87/1a87-T0120-vit.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/T0120-1a87-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -130.116669
Database has 3 sequences with 954 residues.
gzip -f 1a87/T0120-1a87-global.pw.a2m
make 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/1a87-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a87/nostruct-align/1a87.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30057/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:        -191.323654
Database has 3 sequences with 954 residues.
gzip -f 1a87/1a87-T0120-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13524


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13524/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.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/1a/1a87/struct-align/1a87.fssp.a2m.gz (5 sequences, 297 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13524/tmp.a2m.
Dropping 1 (of 5) duplicate sequences with differing IDs
4 sequences left after dropping 1 of 5 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13524/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13524/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-13524/tmp.a2m (4 sequences, 297 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13524/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13524 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1a87
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1a87' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1a87/1a87-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a87/info/1a87.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a87/struct-align/1a87.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13524/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:        -237.457687
Database has 3 sequences with 954 residues.
gzip -f 1a87/1a87-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a87/xxxx-1a87-T0120-local.pw.a2m.gz'.
make[2]: Target `1a87/xxxx-1a87-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1a87/xxxx-1a87-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1qs2A PRED2=1q A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1qs2A/T0120-1qs2A-local.pw.a2m.gz 1qs2A/1qs2A-T0120-local.pw.a2m.gz \
1qs2A/T0120-1qs2A-2track-local.pw.a2m.gz \
1qs2A/T0120-1qs2A-2track-global.pw.a2m.gz \
1qs2A/T0120-1qs2A-vit.pw.a2m.gz 1qs2A/1qs2A-T0120-vit.pw.a2m.gz \
1qs2A/T0120-1qs2A-global.pw.a2m.gz 	1qs2A/1qs2A-T0120-global.pw.a2m.gz \
1qs2A/1qs2A-T0120-fssp-global.pw.a2m.gz \
1qs2A/xxxx-1qs2A-T0120-local.pw.a2m.gz 1qs2A/xxxx-1qs2A-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1qs2A
fixmode 1qs2A
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/T0120-1qs2A-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.818665
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/T0120-1qs2A-local.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/1qs2A-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2371/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:        -267.931030
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/1qs2A-T0120-local.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/T0120-1qs2A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -122.685493
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/T0120-1qs2A-2track-local.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/T0120-1qs2A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -84.903511
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/T0120-1qs2A-2track-global.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/T0120-1qs2A-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.758301
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/T0120-1qs2A-vit.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/1qs2A-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2371/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:        -264.886963
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/1qs2A-T0120-vit.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/T0120-1qs2A-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -119.783669
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/T0120-1qs2A-global.pw.a2m
make 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/1qs2A-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs2A/nostruct-align/1qs2A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2371/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:        -261.720642
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/1qs2A-T0120-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7792


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7792/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.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/1q/1qs2A/struct-align/1qs2A.fssp.a2m.gz (1 sequences, 401 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7792/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7792/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7792/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-7792/tmp.a2m (1 sequences, 401 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7792/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7792 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qs2A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs2A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs2A/1qs2A-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs2A/info/1qs2A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs2A/struct-align/1qs2A.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7792/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:        -413.222015
Database has 3 sequences with 1138 residues.
gzip -f 1qs2A/1qs2A-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qs2A/xxxx-1qs2A-T0120-local.pw.a2m.gz'.
make[2]: Target `1qs2A/xxxx-1qs2A-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1qs2A/xxxx-1qs2A-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1be3B PRED2=1b A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1be3B/T0120-1be3B-local.pw.a2m.gz 1be3B/1be3B-T0120-local.pw.a2m.gz \
1be3B/T0120-1be3B-2track-local.pw.a2m.gz \
1be3B/T0120-1be3B-2track-global.pw.a2m.gz \
1be3B/T0120-1be3B-vit.pw.a2m.gz 1be3B/1be3B-T0120-vit.pw.a2m.gz \
1be3B/T0120-1be3B-global.pw.a2m.gz 	1be3B/1be3B-T0120-global.pw.a2m.gz \
1be3B/1be3B-T0120-fssp-global.pw.a2m.gz \
1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz 1be3B/xxxx-1be3B-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[2]: `1be3B/T0120-1be3B-local.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-local.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-2track-local.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-2track-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-vit.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-vit.pw.a2m.gz' is up to date.
make[2]: `1be3B/T0120-1be3B-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-global.pw.a2m.gz' is up to date.
make[2]: `1be3B/1be3B-T0120-fssp-global.pw.a2m.gz' is up to date.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz'.
make[2]: Target `1be3B/xxxx-1be3B-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1be3B/xxxx-1be3B-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1qs1A PRED2=1q A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1qs1A/T0120-1qs1A-local.pw.a2m.gz 1qs1A/1qs1A-T0120-local.pw.a2m.gz \
1qs1A/T0120-1qs1A-2track-local.pw.a2m.gz \
1qs1A/T0120-1qs1A-2track-global.pw.a2m.gz \
1qs1A/T0120-1qs1A-vit.pw.a2m.gz 1qs1A/1qs1A-T0120-vit.pw.a2m.gz \
1qs1A/T0120-1qs1A-global.pw.a2m.gz 	1qs1A/1qs1A-T0120-global.pw.a2m.gz \
1qs1A/1qs1A-T0120-fssp-global.pw.a2m.gz \
1qs1A/xxxx-1qs1A-T0120-local.pw.a2m.gz 1qs1A/xxxx-1qs1A-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1qs1A
fixmode 1qs1A
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/T0120-1qs1A-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.784271
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/T0120-1qs1A-local.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/1qs1A-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9072/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:        -267.107300
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/1qs1A-T0120-local.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/T0120-1qs1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -120.358620
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/T0120-1qs1A-2track-local.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/T0120-1qs1A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -79.124001
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/T0120-1qs1A-2track-global.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/T0120-1qs1A-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -141.710281
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/T0120-1qs1A-vit.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/1qs1A-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9072/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:        -263.277283
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/1qs1A-T0120-vit.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/T0120-1qs1A-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -117.348656
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/T0120-1qs1A-global.pw.a2m
make 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/1qs1A-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs1A/nostruct-align/1qs1A.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9072/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:        -258.815979
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/1qs1A-T0120-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19395


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19395/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.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/1q/1qs1A/struct-align/1qs1A.fssp.a2m.gz (4 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19395/tmp.a2m.
Dropping 3 (of 4) duplicate sequences with differing IDs
1 sequences left after dropping 3 of 4 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19395/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19395/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-19395/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19395/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19395 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qs1A
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qs1A' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qs1A/1qs1A-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qs1A/info/1qs1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qs1A/struct-align/1qs1A.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19395/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:        -402.581665
Database has 3 sequences with 1200 residues.
gzip -f 1qs1A/1qs1A-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qs1A/xxxx-1qs1A-T0120-local.pw.a2m.gz'.
make[2]: Target `1qs1A/xxxx-1qs1A-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1qs1A/xxxx-1qs1A-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1qcrA PRED2=1q A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1qcrA/T0120-1qcrA-local.pw.a2m.gz 1qcrA/1qcrA-T0120-local.pw.a2m.gz \
1qcrA/T0120-1qcrA-2track-local.pw.a2m.gz \
1qcrA/T0120-1qcrA-2track-global.pw.a2m.gz \
1qcrA/T0120-1qcrA-vit.pw.a2m.gz 1qcrA/1qcrA-T0120-vit.pw.a2m.gz \
1qcrA/T0120-1qcrA-global.pw.a2m.gz 	1qcrA/1qcrA-T0120-global.pw.a2m.gz \
1qcrA/1qcrA-T0120-fssp-global.pw.a2m.gz \
1qcrA/xxxx-1qcrA-T0120-local.pw.a2m.gz 1qcrA/xxxx-1qcrA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1qcrA
fixmode 1qcrA
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/T0120-1qcrA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.367126
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/T0120-1qcrA-local.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/1qcrA-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28296/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:        -229.815384
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/1qcrA-T0120-local.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/T0120-1qcrA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -118.404259
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/T0120-1qcrA-2track-local.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/T0120-1qcrA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -87.565163
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/T0120-1qcrA-2track-global.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/T0120-1qcrA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.460083
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/T0120-1qcrA-vit.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/1qcrA-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28296/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:        -225.332077
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/1qcrA-T0120-vit.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/T0120-1qcrA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -112.378380
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/T0120-1qcrA-global.pw.a2m
make 1qcrA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qcrA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qcrA/1qcrA-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcrA/info/1qcrA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcrA/nostruct-align/1qcrA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28296/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:        -223.506302
Database has 3 sequences with 1228 residues.
gzip -f 1qcrA/1qcrA-T0120-global.pw.a2m
make[2]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1q/1qcrA/struct-align/1qcrA.fssp-w0.5.mod', needed by `1qcrA/1qcrA-T0120-fssp-global.pw.a2m.gz'.
make[2]: Target `1qcrA/1qcrA-T0120-fssp-global.pw.a2m.gz' not remade because of errors.
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcrA/xxxx-1qcrA-T0120-local.pw.a2m.gz'.
make[2]: Target `1qcrA/xxxx-1qcrA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1qcrA/xxxx-1qcrA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1qbeA PRED2=1q A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1qbeA/T0120-1qbeA-local.pw.a2m.gz 1qbeA/1qbeA-T0120-local.pw.a2m.gz \
1qbeA/T0120-1qbeA-2track-local.pw.a2m.gz \
1qbeA/T0120-1qbeA-2track-global.pw.a2m.gz \
1qbeA/T0120-1qbeA-vit.pw.a2m.gz 1qbeA/1qbeA-T0120-vit.pw.a2m.gz \
1qbeA/T0120-1qbeA-global.pw.a2m.gz 	1qbeA/1qbeA-T0120-global.pw.a2m.gz \
1qbeA/1qbeA-T0120-fssp-global.pw.a2m.gz \
1qbeA/xxxx-1qbeA-T0120-local.pw.a2m.gz 1qbeA/xxxx-1qbeA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1qbeA
fixmode 1qbeA
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/T0120-1qbeA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -145.396973
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/T0120-1qbeA-local.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/1qbeA-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19865/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:        -116.036316
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/1qbeA-T0120-local.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/T0120-1qbeA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -118.922127
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/T0120-1qbeA-2track-local.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/T0120-1qbeA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.775490
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/T0120-1qbeA-2track-global.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/T0120-1qbeA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -140.905945
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/T0120-1qbeA-vit.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/1qbeA-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19865/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:        -113.088631
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/1qbeA-T0120-vit.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/T0120-1qbeA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -131.628998
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/T0120-1qbeA-global.pw.a2m
make 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/1qbeA-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qbeA/nostruct-align/1qbeA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19865/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:        -112.061989
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/1qbeA-T0120-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4022


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4022/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.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/1q/1qbeA/struct-align/1qbeA.fssp.a2m.gz (5 sequences, 123 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4022/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-4022/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4022/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-4022/tmp.a2m (3 sequences, 123 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4022/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4022 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qbeA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1qbeA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1qbeA/1qbeA-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qbeA/info/1qbeA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qbeA/struct-align/1qbeA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4022/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:        -68.937660
Database has 3 sequences with 591 residues.
gzip -f 1qbeA/1qbeA-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qbeA/xxxx-1qbeA-T0120-local.pw.a2m.gz'.
make[2]: Target `1qbeA/xxxx-1qbeA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1qbeA/xxxx-1qbeA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)
make -k PRED=1c0aA PRED2=1c A2M=remote-t2k.a2m.gz joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make -k \
1c0aA/T0120-1c0aA-local.pw.a2m.gz 1c0aA/1c0aA-T0120-local.pw.a2m.gz \
1c0aA/T0120-1c0aA-2track-local.pw.a2m.gz \
1c0aA/T0120-1c0aA-2track-global.pw.a2m.gz \
1c0aA/T0120-1c0aA-vit.pw.a2m.gz 1c0aA/1c0aA-T0120-vit.pw.a2m.gz \
1c0aA/T0120-1c0aA-global.pw.a2m.gz 	1c0aA/1c0aA-T0120-global.pw.a2m.gz \
1c0aA/1c0aA-T0120-fssp-global.pw.a2m.gz \
1c0aA/xxxx-1c0aA-T0120-local.pw.a2m.gz 1c0aA/xxxx-1c0aA-T0120-global.pw.a2m.gz
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
mkdir 1c0aA
fixmode 1c0aA
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/T0120-1c0aA-local.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -147.052231
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/T0120-1c0aA-local.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/1c0aA-T0120-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1110/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:        -343.505219
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/1c0aA-T0120-local.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/T0120-1c0aA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -119.866051
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/T0120-1c0aA-2track-local.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/T0120-1c0aA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0120.remote-t2k-w0.5.mod,T0120.remote-t2k-2d.mod \
 -db T0120.seq,T0120.remote-t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.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.remote-t2k-w0.5.mod(21):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/tmp.a2m
T0120.remote-t2k-2d.mod(2045):  Reading track 1 model from MODEL -- Model from 2nd structure file T0120.remote-t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -64.760483
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/T0120-1c0aA-2track-global.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/T0120-1c0aA-vit.pw \
	-i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -143.886566
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/T0120-1c0aA-vit.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/1c0aA-T0120-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1110/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:        -339.855255
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/1c0aA-T0120-vit.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/T0120-1c0aA-global.pw -i T0120.remote-t2k-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0120.remote-t2k-w0.5.mod
T0120.remote-t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10954/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:        -95.333710
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/T0120-1c0aA-global.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/1c0aA-T0120-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c0aA/nostruct-align/1c0aA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1110/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:        -337.873322
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/1c0aA-T0120-global.pw.a2m
make 1c0aA
make[3]: Entering directory `/export/projects/compbio/experiments/casp4/t120'
make[3]: `1c0aA' is up to date.
make[3]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
/projects/compbio/bin/alpha.new/hmmscore 1c0aA/1c0aA-T0120-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c0aA/struct-align/1c0aA.fssp-w0.5.mod -db T0120.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c0aA/info/1c0aA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c0aA/struct-align/1c0aA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c0aA/struct-align/1c0aA.fssp-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13157/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:        -396.253693
Database has 3 sequences with 1506 residues.
gzip -f 1c0aA/1c0aA-T0120-fssp-global.pw.a2m
make[2]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c0aA/xxxx-1c0aA-T0120-local.pw.a2m.gz'.
make[2]: Target `1c0aA/xxxx-1c0aA-T0120-local.pw.a2m.gz' not remade because of errors.
make[2]: Target `1c0aA/xxxx-1c0aA-T0120-global.pw.a2m.gz' not remade because of errors.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make[1]: *** [joint] Error 2
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t120'
make: [joints] Error 2 (ignored)