/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1burA/struct-align/1burA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1burA/struct-align/1burA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-quack-29547 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-quack-29547/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1burA/struct-align/1burA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1b/1burA/struct-align/1burA.fssp.a2m.gz (142 sequences, 464 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-quack-29547/tmp.a2m. Dropping 41 (of 142) duplicate sequences with differing IDs Dropping 21 (of 142) sequences with > 80.0% id 80 sequences left after dropping 62 of 142 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-quack-29547/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-quack-29547/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-quack-29547/tmp.a2m (80 sequences, 464 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-quack-29547/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1burA/struct-align/1burA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1burA Make: Unknown flag argument . Stop. make: *** [1burA/1burA-T0086-fssp-global.pw.a2m.gz] Error 1 make 1burA Make: Unknown flag argument . Stop. make: *** [1burA/T0086-1burA-local.pw.a2m.gz] Error 1 make 1burA Make: Unknown flag argument . Stop. make: *** [1burA/1burA-T0086-local.pw.a2m.gz] Error 1 make 1burA Make: Unknown flag argument . Stop. make: *** [1burA/T0086-1burA-vit.pw.a2m.gz] Error 1 make 1burA Make: Unknown flag argument . Stop. make: *** [1burA/1burA-T0086-vit.pw.a2m.gz] Error 1 make 1burA Make: Unknown flag argument . Stop. make: *** [1burA/T0086-1burA-global.pw.a2m.gz] Error 1 make 1burA Make: Unknown flag argument . Stop. make: *** [1burA/1burA-T0086-global.pw.a2m.gz] Error 1 make: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1burA/xxxx-1burA-T0086-local.pw.a2m.gz'. make: Target `joint' not remade because of errors. /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1nal3/struct-align/1nal3.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1nal3/struct-align/1nal3.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.conf/usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' mkdir 1nal3 fixmode 1nal3 make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/1nal3-T0086-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nal3/struct-align/1nal3.fssp-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/1nal3-T0086-fssp-global.pw.a2m /usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: `1nal3' is up to date. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/T0086-1nal3-local.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/T0086-1nal3-local.pw.a2m /usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: `1nal3' is up to date. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/1nal3-T0086-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nal3/nostruct-align/1nal3.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/1nal3-T0086-local.pw.a2m /usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: `1nal3' is up to date. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/T0086-1nal3-vit.pw \ -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/T0086-1nal3-vit.pw.a2m /usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: `1nal3' is up to date. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/1nal3-T0086-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1nal3/nostruct-align/1nal3.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/1nal3-T0086-vit.pw.a2m /usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: `1nal3' is up to date. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/T0086-1nal3-global.pw -i T0086.t2k-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/T0086-1nal3-global.pw.a2m /usr/local/gnu/bin/make 1nal3 make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' make[1]: `1nal3' is up to date. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86' hmmscore 1nal3/1nal3-T0086-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nal3/nostruct-align/1nal3.t99-w0.5.mod -db T0086.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nal3/info/1nal3.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1nal3/1nal3-T0086-global.pw.a2m