make -k T0121-1-230-blast.rdb T0121-1-230-double-blast.rdb
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t121/t121-1-230'
/projects/compbio/experiments/casp4/scripts/single-blast -q T0121-1-230.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > T0121-1-230-blast.rdb

starting T0121 with E=10
/projects/compbio/experiments/casp4/scripts/double-blast -q T0121-1-230.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > T0121-1-230-double-blast.rdb

starting T0121 with E=0.000050
EXIT CODE 26
T0121 T0121 blasting:
/bin/sh: 24375 Terminated
make[1]: *** [T0121-1-230-double-blast.rdb] Error 143
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t121/t121-1-230'
make: [T0121-1-230.blast-all] Error 2 (ignored)
make -k T0121-1-230.t2k.a2m.gz	\
	T0121-1-230.t2k.pa \
	T0121-1-230.t2k.pa.html \
	T0121-1-230.t2k.2d \
	T0121-1-230.t2k.tree \
	T0121-1-230.t2k_sorted.pa \
	T0121-1-230.t2k.tree.ps \
	T0121-1-230.t2k.tree-unroot.ps 
make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t121/t121-1-230'
/projects/compbio/experiments/models.97/scripts2k/target2k -out T0121-1-230.t2k \
	-seed T0121-1-230.seq \
	-family \
	-thresholds 1e-44,1e-40,1e-25 \
	-prefilter_thresholds 1e-44,1e-40,1e-25 \
	-all


@@@@ chgrp protein /projects/compbio/tmp/target2k-eclipse-24420


@@@@ cp /projects/compbio/experiments/casp4/t121/t121-1-230/T0121-1-230.seq m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:52
# About to count sequences in /projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are
prefilter: 1e-44,	actual: 1e-44
prefilter: 1e-40,	actual: 1e-40
prefilter: 1e-25,	actual: 1e-25
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.5
/projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 551100 reverse_diff= 4
/projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 10000
/projects/compbio/experiments/models.97/scripts2k/target2k: db=/projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_method=1 aweight_exponent=10
/projects/compbio/experiments/models.97/scripts2k/target2k: force_seed=1 constraints=1
/projects/compbio/experiments/models.97/scripts2k/target2k: jump_in=0.2 jump_out=1 fimstrength=1 fimtrans=-1


@@@@ blast-prefilter -out prefilter -seed m0.a2m  -prefilter_thresholds 1e-44,1e-40,1e-25  -db /projects/compbio/data/nrp/nr -blast_max_report 10000


@@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-eclipse-24475
/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are
For /projects/compbio/tmp/target2k-eclipse-24420/prefilter_1.fa,  1e-44
For /projects/compbio/tmp/target2k-eclipse-24420/prefilter_2.fa,  1e-40
For /projects/compbio/tmp/target2k-eclipse-24420/prefilter_3.fa,  1e-25

/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr


@@@@ uniqueseq init -alignfile /projects/compbio/tmp/target2k-eclipse-24420/m0.a2m -a protein -a2mdots 0
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file /projects/compbio/tmp/target2k-eclipse-24420/m0.a2m (1 sequences, 230 columns) as A2M alignment.
Writing sequence output to init.a2m.
No sequences have been dropped.


@@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta  E=1e-25 V=10000 B=0 -gi > 1.fasta-blast.out
Searched 551100 sequences
# parsing wu-blastp output


@@@@ rm -f 1.fasta < /dev/null


@@@@ rm -f 1.fasta-blast.out < /dev/null
# Extracting hits in FASTA format from /projects/compbio/data/nrp/nr


@@@@ rm -rf /projects/compbio/tmp/blast-prefilter-eclipse-24475 < /dev/null


@@@@ modelfromalign unused -alignfile m0.a2m \
             -constraints_from_align 1 -constraints_out m0.cst
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.
# About to count sequences in m0.a2m
# About to count sequences in prefilter_1.fa


@@@@ modelfromalign tmp_1-a -alignfile m0.a2m \
		-insert /projects/compbio/lib/gap1.5.regularizer \
		-aweight_bits 0.8\
		-fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \
    	-aweight_method 1\
	-aweight_exponent 10 -constraints m0.cst -constraints_out tmp_1-a.cst
Reading parameter file /projects/compbio/lib/gap1.5.regularizer
/projects/compbio/lib/gap1.5.regularizer(1):  Reading REGULARIZER: gap1.5.  Weak regularizer, gaps average 1.5, matches average 10
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.


@@@@ hmmscore tmp_1-a -i tmp_1-a.mod -fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\
    	    -dpstyle 0 \
	    -subtract_null 4 -sort 2 \
	-db_size 551100 \
	-simple_threshold -118.533415651609 -Emax 1e-44 \
    	-adpstyle 1 \
	-align_short 0	-mdEmax 1e-44\
	-select_score 4 \
	-select_seq 4 \
	 -select_mdalign 4 -select_md 4 -Motifcutoff 0.0869565217391304 -db prefilter_1.fa -constraints tmp_1-a.cst -constraints_out tmp_1-a-md.cst
Reading parameter file tmp_1-a.mod
tmp_1-a.mod(21):  Reading MODEL --  Model from alignment file m0.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
sh: 24464 Floating exception
*** Error: /projects/compbio/experiments/models.97/scripts2k/target2k: hmmscore to select sequences failed
make[1]: *** [T0121-1-230.t2k.a2m.gz] Error 2
make[1]: Target `T0121-1-230.t2k.pa' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.pa.html' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.2d' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.tree' not remade because of errors.
make[1]: Target `T0121-1-230.t2k_sorted.pa' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.tree.ps' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.tree-unroot.ps' not remade because of errors.
make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t121/t121-1-230'
make: [T0121-1-230.align] Error 2 (ignored)
/projects/compbio/experiments/models.97/scripts2k/target2k -out T0121-1-230.t2k \
	-seed T0121-1-230.seq \
	-family \
	-thresholds 1e-44,1e-40,1e-25 \
	-prefilter_thresholds 1e-44,1e-40,1e-25 \
	-all


@@@@ chgrp protein /projects/compbio/tmp/target2k-eclipse-24544


@@@@ cp /projects/compbio/experiments/casp4/t121/t121-1-230/T0121-1-230.seq m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:52
# About to count sequences in /projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are
prefilter: 1e-44,	actual: 1e-44
prefilter: 1e-40,	actual: 1e-40
prefilter: 1e-25,	actual: 1e-25
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.5
/projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 551100 reverse_diff= 4
/projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 10000
/projects/compbio/experiments/models.97/scripts2k/target2k: db=/projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_method=1 aweight_exponent=10
/projects/compbio/experiments/models.97/scripts2k/target2k: force_seed=1 constraints=1
/projects/compbio/experiments/models.97/scripts2k/target2k: jump_in=0.2 jump_out=1 fimstrength=1 fimtrans=-1


@@@@ blast-prefilter -out prefilter -seed m0.a2m  -prefilter_thresholds 1e-44,1e-40,1e-25  -db /projects/compbio/data/nrp/nr -blast_max_report 10000


@@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-eclipse-19434
/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are
For /projects/compbio/tmp/target2k-eclipse-24544/prefilter_1.fa,  1e-44
For /projects/compbio/tmp/target2k-eclipse-24544/prefilter_2.fa,  1e-40
For /projects/compbio/tmp/target2k-eclipse-24544/prefilter_3.fa,  1e-25

/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr


@@@@ uniqueseq init -alignfile /projects/compbio/tmp/target2k-eclipse-24544/m0.a2m -a protein -a2mdots 0
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file /projects/compbio/tmp/target2k-eclipse-24544/m0.a2m (1 sequences, 230 columns) as A2M alignment.
Writing sequence output to init.a2m.
No sequences have been dropped.


@@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta  E=1e-25 V=10000 B=0 -gi > 1.fasta-blast.out
Searched 551100 sequences
# parsing wu-blastp output


@@@@ rm -f 1.fasta < /dev/null


@@@@ rm -f 1.fasta-blast.out < /dev/null
# Extracting hits in FASTA format from /projects/compbio/data/nrp/nr


@@@@ rm -rf /projects/compbio/tmp/blast-prefilter-eclipse-19434 < /dev/null


@@@@ modelfromalign unused -alignfile m0.a2m \
             -constraints_from_align 1 -constraints_out m0.cst
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.
# About to count sequences in m0.a2m
# About to count sequences in prefilter_1.fa


@@@@ modelfromalign tmp_1-a -alignfile m0.a2m \
		-insert /projects/compbio/lib/gap1.5.regularizer \
		-aweight_bits 0.8\
		-fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \
    	-aweight_method 1\
	-aweight_exponent 10 -constraints m0.cst -constraints_out tmp_1-a.cst
Reading parameter file /projects/compbio/lib/gap1.5.regularizer
/projects/compbio/lib/gap1.5.regularizer(1):  Reading REGULARIZER: gap1.5.  Weak regularizer, gaps average 1.5, matches average 10
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.


@@@@ hmmscore tmp_1-a -i tmp_1-a.mod -fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\
    	    -dpstyle 0 \
	    -subtract_null 4 -sort 2 \
	-db_size 551100 \
	-simple_threshold -118.533415651609 -Emax 1e-44 \
    	-adpstyle 1 \
	-align_short 0	-mdEmax 1e-44\
	-select_score 4 \
	-select_seq 4 \
	 -select_mdalign 4 -select_md 4 -Motifcutoff 0.0869565217391304 -db prefilter_1.fa -constraints tmp_1-a.cst -constraints_out tmp_1-a-md.cst
Reading parameter file tmp_1-a.mod
tmp_1-a.mod(21):  Reading MODEL --  Model from alignment file m0.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
sh: 24543 Floating exception
*** Error: /projects/compbio/experiments/models.97/scripts2k/target2k: hmmscore to select sequences failed
make: *** [T0121-1-230.t2k.a2m.gz] Error 2
make -k T0121-1-230.t2k.a2m.gz	\
	T0121-1-230.t2k.pa \
	T0121-1-230.t2k.pa.html \
	T0121-1-230.t2k.2d \
	T0121-1-230.t2k.tree \
	T0121-1-230.t2k_sorted.pa \
	T0121-1-230.t2k.tree.ps \
	T0121-1-230.t2k.tree-unroot.ps 
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t121/t121-1-230'
/projects/compbio/experiments/models.97/scripts2k/target2k -out T0121-1-230.t2k \
	-seed T0121-1-230.seq \
	-family \
	-thresholds 1e-44,1e-40,1e-25 \
	-prefilter_thresholds 1e-25,1e-20,1e-20 \
	-all


@@@@ chgrp protein /projects/compbio/tmp/target2k-beta-3231


@@@@ cp /export/projects/compbio/experiments/casp4/t121/t121-1-230/T0121-1-230.seq m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:52
# About to count sequences in /projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are
prefilter: 1e-25,	actual: 1e-44
prefilter: 1e-20,	actual: 1e-40
prefilter: 1e-20,	actual: 1e-25
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.5
/projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 551100 reverse_diff= 4
/projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 10000
/projects/compbio/experiments/models.97/scripts2k/target2k: db=/projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_method=1 aweight_exponent=10
/projects/compbio/experiments/models.97/scripts2k/target2k: force_seed=1 constraints=1
/projects/compbio/experiments/models.97/scripts2k/target2k: jump_in=0.2 jump_out=1 fimstrength=1 fimtrans=-1


@@@@ blast-prefilter -out prefilter -seed m0.a2m  -prefilter_thresholds 1e-25,1e-20,1e-20  -db /projects/compbio/data/nrp/nr -blast_max_report 10000


@@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-beta-22385
/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are
For /export/projects/compbio/tmp/target2k-beta-3231/prefilter_1.fa,  1e-25
For /export/projects/compbio/tmp/target2k-beta-3231/prefilter_2.fa,  1e-20
For /export/projects/compbio/tmp/target2k-beta-3231/prefilter_3.fa,  1e-20

/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr


@@@@ uniqueseq init -alignfile /export/projects/compbio/tmp/target2k-beta-3231/m0.a2m -a protein -a2mdots 0
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file /export/projects/compbio/tmp/target2k-beta-3231/m0.a2m (1 sequences, 230 columns) as A2M alignment.
Writing sequence output to init.a2m.
No sequences have been dropped.


@@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta  E=1e-20 V=10000 B=0 -gi > 1.fasta-blast.out
Searched 551100 sequences
# parsing wu-blastp output


@@@@ rm -f 1.fasta < /dev/null


@@@@ rm -f 1.fasta-blast.out < /dev/null
# Extracting hits in FASTA format from /projects/compbio/data/nrp/nr


@@@@ rm -rf /projects/compbio/tmp/blast-prefilter-beta-22385 < /dev/null


@@@@ modelfromalign unused -alignfile m0.a2m \
             -constraints_from_align 1 -constraints_out m0.cst
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.
# About to count sequences in m0.a2m
# About to count sequences in prefilter_1.fa


@@@@ modelfromalign tmp_1-a -alignfile m0.a2m \
		-insert /projects/compbio/lib/gap1.5.regularizer \
		-aweight_bits 0.8\
		-fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \
    	-aweight_method 1\
	-aweight_exponent 10 -constraints m0.cst -constraints_out tmp_1-a.cst
Reading parameter file /projects/compbio/lib/gap1.5.regularizer
/projects/compbio/lib/gap1.5.regularizer(1):  Reading REGULARIZER: gap1.5.  Weak regularizer, gaps average 1.5, matches average 10
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.


@@@@ hmmscore tmp_1-a -i tmp_1-a.mod -fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\
    	    -dpstyle 0 \
	    -subtract_null 4 -sort 2 \
	-db_size 551100 \
	-simple_threshold -118.533415651609 -Emax 1e-44 \
    	-adpstyle 1 \
	-align_short 0	-mdEmax 1e-44\
	-select_score 4 \
	-select_seq 4 \
	 -select_mdalign 4 -select_md 4 -Motifcutoff 0.0869565217391304 -db prefilter_1.fa -constraints tmp_1-a.cst -constraints_out tmp_1-a-md.cst
Reading parameter file tmp_1-a.mod
tmp_1-a.mod(21):  Reading MODEL --  Model from alignment file m0.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
sh: 1982 Floating exception
*** Error: /projects/compbio/experiments/models.97/scripts2k/target2k: hmmscore to select sequences failed
make[1]: *** [T0121-1-230.t2k.a2m.gz] Error 2
make[1]: Target `T0121-1-230.t2k.pa' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.pa.html' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.2d' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.tree' not remade because of errors.
make[1]: Target `T0121-1-230.t2k_sorted.pa' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.tree.ps' not remade because of errors.
make[1]: Target `T0121-1-230.t2k.tree-unroot.ps' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t121/t121-1-230'
make: [T0121-1-230.align] Error 2 (ignored)
/projects/compbio/experiments/models.97/scripts2k/target2k -out T0121-1-230.t2k \
	-seed T0121-1-230.seq \
	-family \
	-thresholds 1e-44,1e-40,1e-25 \
	-prefilter_thresholds 1e-25,1e-20,1e-20 \
	-all


@@@@ chgrp protein /projects/compbio/tmp/target2k-beta-1520


@@@@ cp /export/projects/compbio/experiments/casp4/t121/t121-1-230/T0121-1-230.seq m0.a2m


@@@@ checkseq foo -alphabet protein -db m0.a2m > init.check
SAM: checkseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:52
# About to count sequences in /projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are
prefilter: 1e-25,	actual: 1e-44
prefilter: 1e-20,	actual: 1e-40
prefilter: 1e-20,	actual: 1e-25
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.5
/projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 551100 reverse_diff= 4
/projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 10000
/projects/compbio/experiments/models.97/scripts2k/target2k: db=/projects/compbio/data/nrp/nr
/projects/compbio/experiments/models.97/scripts2k/target2k: aweight_method=1 aweight_exponent=10
/projects/compbio/experiments/models.97/scripts2k/target2k: force_seed=1 constraints=1
/projects/compbio/experiments/models.97/scripts2k/target2k: jump_in=0.2 jump_out=1 fimstrength=1 fimtrans=-1


@@@@ blast-prefilter -out prefilter -seed m0.a2m  -prefilter_thresholds 1e-25,1e-20,1e-20  -db /projects/compbio/data/nrp/nr -blast_max_report 10000


@@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-beta-31482
/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are
For /export/projects/compbio/tmp/target2k-beta-1520/prefilter_1.fa,  1e-25
For /export/projects/compbio/tmp/target2k-beta-1520/prefilter_2.fa,  1e-20
For /export/projects/compbio/tmp/target2k-beta-1520/prefilter_3.fa,  1e-20

/projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr


@@@@ uniqueseq init -alignfile /export/projects/compbio/tmp/target2k-beta-1520/m0.a2m -a protein -a2mdots 0
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file /export/projects/compbio/tmp/target2k-beta-1520/m0.a2m (1 sequences, 230 columns) as A2M alignment.
Writing sequence output to init.a2m.
No sequences have been dropped.


@@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta  E=1e-20 V=10000 B=0 -gi > 1.fasta-blast.out
Searched 551100 sequences
# parsing wu-blastp output


@@@@ rm -f 1.fasta < /dev/null


@@@@ rm -f 1.fasta-blast.out < /dev/null
# Extracting hits in FASTA format from /projects/compbio/data/nrp/nr


@@@@ rm -rf /projects/compbio/tmp/blast-prefilter-beta-31482 < /dev/null


@@@@ modelfromalign unused -alignfile m0.a2m \
             -constraints_from_align 1 -constraints_out m0.cst
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.
# About to count sequences in m0.a2m
# About to count sequences in prefilter_1.fa


@@@@ modelfromalign tmp_1-a -alignfile m0.a2m \
		-insert /projects/compbio/lib/gap1.5.regularizer \
		-aweight_bits 0.8\
		-fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1 \
    	-aweight_method 1\
	-aweight_exponent 10 -constraints m0.cst -constraints_out tmp_1-a.cst
Reading parameter file /projects/compbio/lib/gap1.5.regularizer
/projects/compbio/lib/gap1.5.regularizer(1):  Reading REGULARIZER: gap1.5.  Weak regularizer, gaps average 1.5, matches average 10
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file m0.a2m (1 sequences, 230 columns) as A2M alignment.


@@@@ hmmscore tmp_1-a -i tmp_1-a.mod -fimtrans -1\
    	-fimstrength 1\
        -ins_jump_conf 1 \
	-match_jump_conf 1 \
	-del_jump_conf 1 \
	-binary_output 1\
	-prior_library /projects/compbio/lib/recode3.20comp \
	-a2mdots 0 \
	-a protein \
        -sw 2 -jump_in_prob 0.2 -jump_out_prob 1\
    	    -dpstyle 0 \
	    -subtract_null 4 -sort 2 \
	-db_size 551100 \
	-simple_threshold -118.533415651609 -Emax 1e-44 \
    	-adpstyle 1 \
	-align_short 0	-mdEmax 1e-44\
	-select_score 4 \
	-select_seq 4 \
	 -select_mdalign 4 -select_md 4 -Motifcutoff 0.0869565217391304 -db prefilter_1.fa -constraints tmp_1-a.cst -constraints_out tmp_1-a-md.cst
Reading parameter file tmp_1-a.mod
tmp_1-a.mod(21):  Reading MODEL --  Model from alignment file m0.a2m
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
Calculating Distances (. = 1000 sequences)
sh: 1088 Floating exception
*** Error: /projects/compbio/experiments/models.97/scripts2k/target2k: hmmscore to select sequences failed
make: *** [T0121-1-230.t2k.a2m.gz] Error 2