make -k T0100-blast.rdb T0100-double-blast.rdb make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100' /projects/compbio/experiments/casp4/scripts/single-blast -q T0100.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > T0100-blast.rdb starting T0100 with E=10 /projects/compbio/experiments/casp4/scripts/double-blast -q T0100.seq -interdb /projects/compbio/data/nrp/nr -db /projects/compbio/data/pdb/all-protein > T0100-double-blast.rdb starting T0100 with E=0.000050 T0100 T0100 blasting: T0100 gi|130345|sp|P17872|PME_ASPTU_29:286 blasting: T0100 gi|130345|sp|P17872|PME_ASPTU_257:321 blasting: T0100 gi|1172538|sp|P41510|PME_BRANA_379:499 blasting: T0100 gi|82097|pir||S00629_136:280 blasting: T0100 gi|82097|pir||S00629_61:225 blasting: T0100 gi|100008|pir||S25171_103:217 blasting: T0100 gi|100008|pir||S25171_1:160 blasting: T0100 gi|100010|pir||S25172_105:215 blasting: T0100 gi|130346|sp|P07863|PMEA_ERWCH_25:366 blasting: T0100 gi|82096|pir||A25010_81:198 blasting: T0100 gi|82096|pir||A25010_4:51 blasting: T0100 gi|130347|sp|P24791|PME_BURSO_81:394 blasting: T0100 gi|478290|pir||JN0799_25:366 blasting: T0100 gi|6174913|sp|P14280|PME1_LYCES_225:452 blasting: T0100 gi|2507165|sp|P09607|PM21_LYCES_312:456 blasting: T0100 gi|2507165|sp|P09607|PM21_LYCES_237:401 blasting: T0100 gi|6093743|sp|Q43043|PME_PETIN_117:277 blasting: T0100 gi|6093743|sp|Q43043|PME_PETIN_58:222 blasting: T0100 gi|6093743|sp|Q43043|PME_PETIN_230:328 blasting: T0100 gi|6093736|sp|Q43867|PME1_ARATH_385:499 blasting: T0100 gi|6093739|sp|Q43111|PME3_PHAVU_270:493 blasting: T0100 gi|6093739|sp|Q43111|PME3_PHAVU_519:571 blasting: T0100 gi|6093742|sp|Q42920|PME_MEDSA_162:349 blasting: T0100 gi|6093742|sp|Q42920|PME_MEDSA_381:421 blasting: T0100 gi|6093737|sp|Q42534|PME2_ARATH_302:490 blasting: T0100 gi|1084429|pir||S46296_59:219 blasting: T0100 gi|1084429|pir||S46296_6:164 blasting: T0100 gi|7447367|pir||S78456_112:257 blasting: T0100 gi|7447367|pir||S78456_7:171 blasting: T0100 gi|7447367|pir||S78456_231:278 blasting: T0100 gi|2499456|sp|Q47474|PMEB_ERWCH_197:386 blasting: T0100 gi|6093744|sp|Q43062|PME_PRUPE_239:511 blasting: T0100 gi|6093744|sp|Q43062|PME_PRUPE_212:372 blasting: T0100 gi|6093740|sp|Q43143|PMEU_LYCES_377:491 blasting: T0100 gi|6093740|sp|Q43143|PMEU_LYCES_276:436 blasting: T0100 gi|2499454|sp|Q12535|PME_ASPAC_29:323 blasting: T0100 gi|1256263|gb|AAB67739.1|_312:456 blasting: T0100 gi|1256263|gb|AAB67739.1|_237:401 blasting: T0100 gi|1256267|gb|AAB67740.1|_109:336 blasting: T0100 gi|7489089|pir||T16974_69:183 blasting: T0100 gi|7489090|pir||T16975_70:251 blasting: T0100 gi|7489090|pir||T16975_1:223 blasting: T0100 gi|7489090|pir||T16975_226:303 blasting: T0100 gi|7489091|pir||T16976_70:251 blasting: T0100 gi|7489091|pir||T16976_1:223 blasting: T0100 gi|7489091|pir||T16976_226:303 blasting: T0100 gi|7489092|pir||T16977_29:210 blasting: T0100 gi|7447362|pir||T07181_102:216 blasting: T0100 gi|7447362|pir||T07181_1:215 blasting: T0100 gi|7447363|pir||T07183_105:219 blasting: T0100 gi|7447363|pir||T07183_1:164 blasting: T0100 gi|6093741|sp|Q42608|PME_BRACM_366:486 blasting: T0100 gi|7447385|pir||T09823_48:215 blasting: T0100 gi|1552379|emb|CAA69348.1|_134:377 blasting: T0100 gi|6093734|sp|Q96575|PM22_LYCES_312:456 blasting: T0100 gi|6093734|sp|Q96575|PM22_LYCES_237:401 blasting: T0100 gi|6093738|sp|Q96576|PME3_LYCES_334:470 blasting: T0100 gi|6093738|sp|Q96576|PME3_LYCES_232:395 blasting: T0100 gi|1617588|gb|AAB38794.1|_157:345 blasting: T0100 gi|1617588|gb|AAB38794.1|_126:290 blasting: T0100 gi|1932927|gb|AAB51702.1|_4:97 blasting: T0100 gi|6174912|sp|O04886|PME1_CITSI_338:492 blasting: T0100 gi|6174912|sp|O04886|PME1_CITSI_269:437 blasting: T0100 gi|6174914|sp|O04887|PME2_CITSI_267:454 blasting: T0100 gi|6174914|sp|O04887|PME2_CITSI_202:364 blasting: T0100 gi|7447380|pir||T10492_338:492 blasting: T0100 gi|7447380|pir||T10492_269:437 blasting: T0100 gi|7447381|pir||T10494_267:454 blasting: T0100 gi|7447381|pir||T10494_202:364 blasting: T0100 gi|2121037|pir||S70913_99:178 blasting: T0100 gi|2121037|pir||S70913_5:116 blasting: T0100 gi|7485253|pir||T01761_70:146 blasting: T0100 gi|7447384|pir||T04359_356:470 blasting: T0100 gi|7485174|pir||G71425_468:692 blasting: T0100 gi|7485174|pir||G71425_391:498 blasting: T0100 gi|2275206|gb|AAB63828.1|_60:161 blasting: T0100 gi|2388565|gb|AAB71446.1|_162:351 blasting: T0100 gi|7447370|pir||T00429_230:412 blasting: T0100 gi|7447370|pir||T00429_164:182 blasting: T0100 gi|7447372|pir||T06468_346:491 blasting: T0100 gi|7447372|pir||T06468_241:400 blasting: T0100 gi|7447372|pir||T06468_384:512 blasting: T0100 gi|2583131|gb|AAB82640.1|_268:446 blasting: T0100 gi|2583131|gb|AAB82640.1|_205:365 blasting: T0100 gi|7447369|pir||T00977_304:483 blasting: T0100 gi|7447376|pir||T00978_235:402 blasting: T0100 gi|2829892|gb|AAC00600.1|_289:470 blasting: T0100 gi|2895510|gb|AAC72288.1|_312:500 blasting: T0100 gi|2895510|gb|AAC72288.1|_285:445 blasting: T0100 gi|2895512|gb|AAC02973.1|_2:75 blasting: T0100 gi|7447371|pir||T06374_346:491 blasting: T0100 gi|7447371|pir||T06374_241:400 blasting: T0100 gi|7447371|pir||T06374_384:512 blasting: T0100 gi|7488000|pir||T00536_101:288 blasting: T0100 gi|7447365|pir||T01318_312:426 blasting: T0100 gi|7447366|pir||T01317_334:494 blasting: T0100 gi|7447388|pir||T01347_233:425 blasting: T0100 gi|7447391|pir||T01870_216:449 blasting: T0100 gi|3342904|gb|AAC27719.1|_276:501 blasting: T0100 gi|7447389|pir||T01418_294:440 blasting: T0100 gi|7447386|pir||T02183_390:510 blasting: T0100 gi|7447387|pir||T02184_383:503 blasting: T0100 gi|7447387|pir||T02184_265:300 blasting: T0100 gi|4415915|gb|AAD20146.1|_40:257 blasting: T0100 gi|4415916|gb|AAD20147.1|_101:317 blasting: T0100 gi|4415916|gb|AAD20147.1|_309:384 blasting: T0100 gi|7447375|pir||T05202_237:398 blasting: T0100 gi|7447375|pir||T05202_162:328 blasting: T0100 gi|7447375|pir||T05202_415:477 blasting: T0100 gi|7447390|pir||T05203_348:517 blasting: T0100 gi|4514622|dbj|BAA75474.1|_29:277 blasting: T0100 gi|4531441|gb|AAD22126.1|AC006224_8_281:424 blasting: T0100 gi|4567229|gb|AAD23644.1|AC007119_10_152:328 blasting: T0100 gi|5442422|gb|AAD43340.1|AF159252_1_45:257 blasting: T0100 gi|5442422|gb|AAD43340.1|AF159252_1_262:331 blasting: T0100 gi|7447382|pir||T12995_386:584 blasting: T0100 gi|5566248|gb|AAD45347.1|_2:96 blasting: T0100 gi|5566252|gb|AAD45348.1|_1:40 blasting: T0100 gi|5734773|gb|AAD50038.1|AC007980_3_177:339 blasting: T0100 gi|5802953|gb|AAD51853.1|AF178989_1_40:254 blasting: T0100 gi|5922617|dbj|BAA84618.1|_335:517 blasting: T0100 gi|5922617|dbj|BAA84618.1|_300:459 blasting: T0100 gi|5922617|dbj|BAA84618.1|_554:564 blasting: T0100 gi|6048277|emb|CAB57457.2|_49:247 blasting: T0100 gi|6056392|gb|AAF02856.1|AC009324_5_270:495 blasting: T0100 gi|6056422|gb|AAF02886.1|AC009525_20_268:486 blasting: T0100 gi|6093122|emb|CAB58974.1|_390:510 blasting: T0100 gi|6358800|gb|AAF07380.1|AC010675_3_49:263 blasting: T0100 gi|6554191|gb|AAF16637.1|AC011661_15_17:159 blasting: T0100 gi|6554192|gb|AAF16638.1|AC011661_16_215:539 blasting: T0100 gi|6554203|gb|AAF16649.1|AC011661_27_120:264 blasting: T0100 gi|6554203|gb|AAF16649.1|AC011661_27_47:209 blasting: T0100 gi|6630558|gb|AAF19577.1|AC011708_20_311:571 blasting: T0100 gi|6630559|gb|AAF19578.1|AC011708_21_360:480 blasting: T0100 gi|6630559|gb|AAF19578.1|AC011708_21_479:551 blasting: T0100 gi|6688851|emb|CAB65290.1|_283:449 blasting: T0100 gi|6688851|emb|CAB65290.1|_231:395 blasting: T0100 gi|6688851|emb|CAB65290.1|_467:499 blasting: T0100 gi|6688852|emb|CAB65291.1|_301:467 blasting: T0100 gi|6688852|emb|CAB65291.1|_503:539 blasting: T0100 gi|6689890|gb|AAF23891.1|_322:436 blasting: T0100 gi|6689890|gb|AAF23891.1|_457:516 blasting: T0100 gi|6689892|gb|AAF23892.1|AF152172_1_370:484 blasting: T0100 gi|6689892|gb|AAF23892.1|AF152172_1_269:429 blasting: T0100 gi|6689892|gb|AAF23892.1|AF152172_1_489:564 blasting: T0100 gi|6714448|gb|AAF26135.1|AC011620_11_277:450 blasting: T0100 gi|6714449|gb|AAF26136.1|AC011620_12_343:474 blasting: T0100 gi|6714449|gb|AAF26136.1|AC011620_12_29:91 blasting: T0100 gi|6714532|dbj|BAA89480.1|_339:506 blasting: T0100 gi|6723392|emb|CAB66401.1|_390:504 blasting: T0100 gi|6899927|emb|CAB71877.1|_383:503 blasting: T0100 gi|7025485|gb|AAF35897.1|AF229849_1_38:264 blasting: T0100 gi|7329683|emb|CAB82677.1|_273:404 blasting: T0100 gi|7447368|pir||S72525_108:252 blasting: T0100 gi|7447368|pir||S72525_4:167 blasting: T0100 gi|7447368|pir||S72525_226:273 blasting: T0100 gi|7529744|emb|CAB86929.1|_266:436 blasting: T0100 gi|7549630|gb|AAF63815.1|_282:552 blasting: T0100 gi|7549630|gb|AAF63815.1|_251:416 blasting: T0100 gi|7576179|emb|CAB87930.1|_54:267 blasting: T0100 gi|7576180|emb|CAB87931.1|_66:228 blasting: T0100 gi|7576180|emb|CAB87931.1|_130:286 blasting: T0100 gi|7576181|emb|CAB87932.1|_66:320 blasting: T0100 gi|7649367|emb|CAB89048.1|_255:476 blasting: T0100 gi|7649367|emb|CAB89048.1|_211:378 blasting: T0100 gi|7670030|dbj|BAA94984.1|_108:246 blasting: T0100 gi|7670030|dbj|BAA94984.1|_296:337 blasting: T0100 gi|7671413|emb|CAB89354.1|_347:469 blasting: T0100 gi|7671413|emb|CAB89354.1|_246:406 blasting: make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100' make -k T0100.t2k.a2m.gz \ T0100.t2k.pa \ T0100.t2k.pa.html \ T0100.t2k.2d \ T0100.t2k.tree \ T0100.t2k_sorted.pa \ T0100.t2k.tree.ps \ T0100.t2k.tree-unroot.ps make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t100' /projects/compbio/experiments/models.97/scripts2k/target2k -out T0100.t2k \ -seed T0100.seq \ -all @@@@ chgrp protein /projects/compbio/tmp/target2k-beta-4494 @@@@ cp /export/projects/compbio/experiments/casp4/t100/T0100.seq m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:44 # About to count sequences in /projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are prefilter: 0.01, actual: 0.0001 prefilter: 1, actual: 0.0002 prefilter: 10, actual: 0.001 prefilter: 400, actual: 0.005 /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.6, 0.5 /projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 509169 reverse_diff= 4 /projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 20000 /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 0.01,1,10,400 -db /projects/compbio/data/nrp/nr -blast_max_report 20000 @@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-beta-7687 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /export/projects/compbio/tmp/target2k-beta-4494/prefilter_1.fa, 0.01 For /export/projects/compbio/tmp/target2k-beta-4494/prefilter_2.fa, 1 For /export/projects/compbio/tmp/target2k-beta-4494/prefilter_3.fa, 10 For /export/projects/compbio/tmp/target2k-beta-4494/prefilter_4.fa, 400 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr @@@@ uniqueseq init -alignfile /export/projects/compbio/tmp/target2k-beta-4494/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /export/projects/compbio/tmp/target2k-beta-4494/m0.a2m (1 sequences, 342 columns) as A2M alignment. Writing sequence output to init.a2m. No sequences have been droppd. @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta E=400 V=20000 B=0 -gi > 1.fasta-blast.out Searched 509169 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-7687 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (1 sequences, 342 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (1 sequences, 342 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 509169 \ -simple_threshold -26.3508756357805 -Emax 0.0001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -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(23): Reading MODEL -- Model from alignment file m0.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -76.715164 Database has 116 sequences with 49912 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_1-a.mult (105 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_1-a.mstat Writing sequence output to tmp_1-a-sort.a2m. @@@@ cat m0.a2m tmp_1-a-sort.a2m > tmp_1-a.train.seq @@@@ cat m0.cst tmp_1-a-md.cst > tmp_1-a.train.cst # About to count sequences in tmp_1-a.train.seq # num_seqs=106 nll_thresh=-22.3508756357805 frac_id=0.913386926069905 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.913386926069905 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_1-a.train.seq (106 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 5 (of 106) duplicate sequences with differing IDs Dropping 18 (of 106) sequences with > 91.3% id 83 sequences left after dropping 23 of 106 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_1-a.train.seq \ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_1-a.train.seq (83 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_1-b -insert 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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_1-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/gap1.5.regularizer -sequence_weights tmp_1-a.w -constraints tmp_1-a.train.cst Reading parameter file tmp_1-a.mod tmp_1-a.mod(23): Reading MODEL -- Model from alignment file m0.a2m Command line option(48): internal_weight has already been set. Using 0. 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: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -966.01 43.63 -225.70 133.90 19 0 343 @@@@ hmmscore tmp_1-b -i tmp_1-b.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 509169 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -26.3508756357805 -Emax 0.0001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 0.0001 -constraints tmp_1-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.cst Reading parameter file tmp_1-b.mod tmp_1-b.mod(20): Reading MODEL -- Final model for run tmp_1-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -294.214355 Database has 111 sequences with 49621 residues. @@@@ cp -f tmp_1-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.a2m \ -insert /projects/compbio/lib/stiff-gap5.regularizer \ -aweight_bits 0.7\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.cst -constraints_out tmp_2-a.cst Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.a2m (113 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_2-a -i tmp_2-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 509169 \ -simple_threshold -25.6577284550241 -Emax 0.0002 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.0002\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_2.fa -constraints tmp_2-a.cst -constraints_out tmp_2-a-md.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -256.255157 Database has 121 sequences with 52123 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_2-a.mult (120 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_2-a.mstat Writing sequence output to tmp_2-a-sort.a2m. @@@@ cat m0.a2m tmp_2-a-sort.a2m > tmp_2-a.train.seq @@@@ cat m0.cst tmp_2-a-md.cst > tmp_2-a.train.cst # About to count sequences in tmp_2-a.train.seq # num_seqs=121 nll_thresh=-21.6577284550241 frac_id=0.885531513713558 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.885531513713558 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_2-a.train.seq (121 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 4 (of 121) duplicate sequences with differing IDs Dropping 33 (of 121) sequences with > 88.6% id 84 sequences left after dropping 37 of 121 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_2-a.train.seq \ -aweight_bits 0.7\ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_2-a.train.seq (84 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_2-b -insert tmp_2-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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_2-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/stiff-gap5.regularizer -sequence_weights tmp_2-a.w -constraints tmp_2-a.train.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_1.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -965.14 1.00 -244.23 109.11 10 0 343 @@@@ hmmscore tmp_2-b -i tmp_2-b.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 509169 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -25.6577284550241 -Emax 0.0002 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 0.0002 -constraints tmp_2-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.cst Reading parameter file tmp_2-b.mod tmp_2-b.mod(20): Reading MODEL -- Final model for run tmp_2-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -258.600586 Database has 120 sequences with 51254 residues. @@@@ cp -f tmp_2-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.a2m \ -insert /projects/compbio/lib/stiff-gap5.regularizer \ -aweight_bits 0.6\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.cst -constraints_out tmp_3-a.cst Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.a2m (121 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_3-a -i tmp_3-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 509169 \ -simple_threshold -24.0482905410188 -Emax 0.001 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.001\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_3.fa -constraints tmp_3-a.cst -constraints_out tmp_3-a-md.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -223.286865 Database has 134 sequences with 58206 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_3-a.mult (120 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_3-a.mstat Writing sequence output to tmp_3-a-sort.a2m. @@@@ cat m0.a2m tmp_3-a-sort.a2m > tmp_3-a.train.seq @@@@ cat m0.cst tmp_3-a-md.cst > tmp_3-a.train.cst # About to count sequences in tmp_3-a.train.seq # num_seqs=121 nll_thresh=-20.0482905410188 frac_id=0.871855366723561 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.871855366723561 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_3-a.train.seq (121 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 4 (of 121) duplicate sequences with differing IDs Dropping 36 (of 121) sequences with > 87.2% id 81 sequences left after dropping 40 of 121 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_3-a.train.seq \ -aweight_bits 0.6\ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_3-a.train.seq (81 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_3-b -insert tmp_3-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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_3-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/stiff-gap5.regularizer -sequence_weights tmp_3-a.w -constraints tmp_3-a.train.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_2.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -966.37 5.29 -228.94 110.13 9 0 343 @@@@ hmmscore tmp_3-b -i tmp_3-b.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 509169 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -24.0482905410188 -Emax 0.001 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 0.001 -constraints tmp_3-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.cst Reading parameter file tmp_3-b.mod tmp_3-b.mod(20): Reading MODEL -- Final model for run tmp_3-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -241.284683 Database has 121 sequences with 51635 residues. @@@@ cp -f tmp_3-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.a2m # About to count sequences in prefilter_4.fa @@@@ modelfromalign tmp_4-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.5\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.cst -constraints_out tmp_4-a.cst 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.a2m (122 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_4-a -i tmp_4-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 509169 \ -simple_threshold -22.4388526207288 -Emax 0.005 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_4.fa -constraints tmp_4-a.cst -constraints_out tmp_4-a-md.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.516529 Database has 541 sequences with 161048 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_4-a.mult (121 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_4-a.mstat Writing sequence output to tmp_4-a-sort.a2m. @@@@ cat m0.a2m tmp_4-a-sort.a2m > tmp_4-a.train.seq @@@@ cat m0.cst tmp_4-a-md.cst > tmp_4-a.train.cst # About to count sequences in tmp_4-a.train.seq # num_seqs=122 nll_thresh=-18.4388526207288 frac_id=0.855412667563766 @@@@ uniqueseq thinned_tmp -alignfile tmp_4-a.train.seq -a protein \ -percent_id 0.855412667563766 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_4-a.train.seq (122 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 3 (of 122) duplicate sequences with differing IDs Dropping 39 (of 122) sequences with > 85.5% id 80 sequences left after dropping 42 of 122 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_4-a.train.seq \ -aweight_bits 0.5\ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_4-a.train.seq (80 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_4-b -insert tmp_4-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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_4-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/fssp-trained.regularizer -sequence_weights tmp_4-a.w -constraints tmp_4-a.train.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_3.a2m Command line option(48): internal_weight has already been set. Using 0. 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: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -967.15 18.48 -228.59 114.22 10 0 343 @@@@ hmmscore tmp_4-b -i tmp_4-b.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 509169 \ -db m0.a2m -db tmp_4-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -22.4388526207288 -Emax 0.005 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 0.005 -constraints tmp_4-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.t2k_4.cst Reading parameter file tmp_4-b.mod tmp_4-b.mod(20): Reading MODEL -- Final model for run tmp_4-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -241.238434 Database has 122 sequences with 51679 residues. @@@@ cp -f tmp_4-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.t2k_4.a2m @@@@ modelfromalign tmp_5-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.t2k_4.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.5\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.t2k_4.cst -constraints_out tmp_5-a.cst 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_4.a2m (122 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_5-a -i tmp_5-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 509169 \ -simple_threshold -22.4388526207288 -Emax 0.005 \ -adpstyle 5 \ -align_short 0 -mdEmax 0.005\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_4.fa -constraints tmp_5-a.cst -constraints_out tmp_5-a-md.cst Reading parameter file tmp_5-a.mod tmp_5-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k_4.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.359528 Database has 541 sequences with 161048 residues. @@@@ sortseq tmp_5-a-sort -alignfile tmp_5-a.mult \ -NLLfile tmp_5-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_5-a.mult (118 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_5-a.mstat Writing sequence output to tmp_5-a-sort.a2m. @@@@ cat m0.a2m tmp_5-a-sort.a2m > tmp_5-a.train.seq @@@@ cat m0.cst tmp_5-a-md.cst > tmp_5-a.train.cst @@@@ cp tmp_5-a.train.seq /export/projects/compbio/experiments/casp4/t100/T0100.t2k.a2m @@@@ cp tmp_5-a.train.cst /export/projects/compbio/experiments/casp4/t100/T0100.t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-beta-4494 < /dev/null gzip -f T0100.t2k.a2m T0100.t2k_*.a2m prettyalign T0100.t2k.a2m.gz -m8 -i -n -L3333 > T0100.t2k.pa SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 gunzip -c T0100.t2k.a2m.gz > tmp.a2m a2m2html -a2m_in tmp.a2m -retrieve > T0100.t2k.pa.html SAM: /projects/compbio/bin/alpha/prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 rm tmp.a2m echo ReadNeuralNet /projects/compbio/usr/karplus/predict-2nd/testing/networks/overrep-2500-IDaa13-5-9-7-10-5-10-11-ehl2-seeded4-stride-trained.net > tmp.script echo ReadA2M T0100.t2k.a2m.gz >> tmp.script echo PrintPrediction T0100.t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0100.t2k.2d.seq >> tmp.script echo PrintRDB T0100.t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-9-7-10-5-10-11-ehl2-seeded4-stride-trained.net # command:# Reading A2M format from T0100.t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0100.t2k.a2m with 119 sequences, total weight= 30.0563 avg weight= 0.252574 46 iterations Regularizing alignment for T0100.t2k.a2m.gz # After reading T0100.t2k.a2m.gz, have 342 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0100.t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0100.t2k.2d.seq # command:# Network initialization done # Printing prediction to T0100.t2k.2d.rdb # command:rm tmp.script gunzip -f T0100.t2k.a2m.gz /projects/compbio/usr/karplus/src/phytree/phytree -o -i -r flat T0100.t2k T0100.t2k.a2m /projects/compbio/lib/recode2.20comp Prior library /projects/compbio/lib/recode2.20comp read. Reading alignment file T0100.t2k.a2m (119 sequences) as A2M alignment. Alignment T0100.t2k.a2m read. Adding sequences:0 10 20 30 40 50 60 70 80 90 100 110 One dot for every 10 merges: ............ Merges done. CPU = user 0: 3: 3 system 0: 0: 0 gzip -f T0100.t2k.a2m gzip -f T0100.t2k_sorted.a2m rm T0100.t2k.phytrace T0100.t2k.tree_weight prettyalign T0100.t2k_sorted.a2m.gz -m8 -i -n -L3333 > T0100.t2k_sorted.pa SAM: prettyalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:15 /projects/compbio/usr/karplus/src/phytree/dg T0100.t2k.tree /projects/compbio/usr/karplus/src/phytree/dtree T0100.t2k.tree make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t100' /projects/compbio/experiments/models.97/scripts99/score-target -alignment T0100.t2k.a2m.gz -build w0.5 \ -db /projects/compbio/data/pdb/all-protein \ -Emax 40.0 \ -viterbi 0 -sw_score 2 \ -output T0100.t2k-w0.5-pdb.rdb PATH=.:/projects/compbio/experiments/models.97/scripts99:/projects/compbio/bin:/projects/compbio/bin/alpha:/projects/compbio/bin/hmmscripts:/projects/compbio/bin/scripts:/sbin:/usr/sbin:/bin:/usr/bin:/usr/local/gnu/bin:/usr/local/share/request/bin:/usr/local/bin @@@@ mkdir /projects/compbio/tmp/score-target-13565 @@@@ mkdir /projects/compbio/tmp/score-target-13565/for-scorescript @@@@ /projects/compbio/experiments/models.97/scripts99/score-mods-vs-seqs.pl -root_tmp /projects/compbio/tmp/score-target-13565/for-scorescript -a2msfile /projects/compbio/tmp/score-target-13565/score-target.a2m \ -buildscript /projects/compbio/bin/scripts/w0.5 -seqfile /projects/compbio/data/pdb/all-protein -Emax 40.0 -viterbi 0 \ -sw_score 2 -output /projects/compbio/tmp/score-target-13565/score-target.op @@@@ chgrp protein /projects/compbio/tmp/score-target-13565/for-scorescript/split-tmp @@@@ chgrp protein /projects/compbio/tmp/score-target-13565/for-scorescript/split-tmp @@@@ /projects/compbio/bin/scripts/w0.5 /export/projects/compbio/experiments/casp4/t100/T0100.t2k.a2m.gz /projects/compbio/tmp/score-target-13565/for-scorescript/split-tmp/beta-28128/T0100.t2k.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14292 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14292/tmp -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.t2k.a2m.gz (119 sequences, 342 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14292/tmp.a2m. Dropping 3 (of 119) duplicate sequences with differing IDs Dropping 43 (of 119) sequences with > 80.0% id 73 sequences left after dropping 46 of 119 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14292/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14292/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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14292/tmp.a2m (73 sequences, 342 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14292/tmp.mod /projects/compbio/tmp/score-target-13565/for-scorescript/split-tmp/beta-28128/T0100.t2k.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14292 m0.a2m @@@@ checkseq foo -alphabet protein -db m0.a2m > init.check SAM: checkseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:44 # About to count sequences in /projects/compbio/data/nrp/nr /projects/compbio/experiments/models.97/scripts2k/target2k: E-value thresholds used are prefilter: 1000, actual: 0.1 prefilter: 1000, actual: 1 prefilter: 2000, actual: 10 /projects/compbio/experiments/models.97/scripts2k/target2k: aweight_bits are 0.8, 0.7, 0.6 /projects/compbio/experiments/models.97/scripts2k/target2k: db_size= 509169 reverse_diff= 4 /projects/compbio/experiments/models.97/scripts2k/target2k: blast_max_report= 20000 /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 1000,1000,2000 -db /projects/compbio/data/nrp/nr -blast_max_report 20000 @@@@ chgrp protein /projects/compbio/tmp/blast-prefilter-beta-22590 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: E-value thresholds used are For /export/projects/compbio/tmp/target2k-beta-3276/prefilter_1.fa, 1000 For /export/projects/compbio/tmp/target2k-beta-3276/prefilter_2.fa, 1000 For /export/projects/compbio/tmp/target2k-beta-3276/prefilter_3.fa, 2000 /projects/compbio/experiments/models.97/scripts2k/blast-prefilter: db=/projects/compbio/data/nrp/nr @@@@ uniqueseq init -alignfile /export/projects/compbio/tmp/target2k-beta-3276/m0.a2m -a protein -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /export/projects/compbio/tmp/target2k-beta-3276/m0.a2m (119 sequences, 342 columns) as A2M alignment. Writing sequence output to init.a2m. Dropping 3 (of 119) duplicate sequences with differing IDs Dropping 2 (of 119) sequences with > 100.0% id 114 sequences left after dropping 5 of 119 sequences. @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 1.fasta E=2000 V=20000 B=0 -gi > 1.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 1.fasta < /dev/null @@@@ rm -f 1.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 2.fasta E=2000 V=20000 B=0 -gi > 2.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 2.fasta < /dev/null @@@@ rm -f 2.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 3.fasta E=2000 V=20000 B=0 -gi > 3.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 3.fasta < /dev/null @@@@ rm -f 3.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 4.fasta E=2000 V=20000 B=0 -gi > 4.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 4.fasta < /dev/null @@@@ rm -f 4.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 5.fasta E=2000 V=20000 B=0 -gi > 5.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 5.fasta < /dev/null @@@@ rm -f 5.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 6.fasta E=2000 V=20000 B=0 -gi > 6.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 6.fasta < /dev/null @@@@ rm -f 6.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 7.fasta E=2000 V=20000 B=0 -gi > 7.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 7.fasta < /dev/null @@@@ rm -f 7.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 8.fasta E=2000 V=20000 B=0 -gi > 8.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 8.fasta < /dev/null @@@@ rm -f 8.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 9.fasta E=2000 V=20000 B=0 -gi > 9.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 9.fasta < /dev/null @@@@ rm -f 9.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 10.fasta E=2000 V=20000 B=0 -gi > 10.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 10.fasta < /dev/null @@@@ rm -f 10.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 11.fasta E=2000 V=20000 B=0 -gi > 11.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 11.fasta < /dev/null @@@@ rm -f 11.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 12.fasta E=2000 V=20000 B=0 -gi > 12.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 12.fasta < /dev/null @@@@ rm -f 12.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 13.fasta E=2000 V=20000 B=0 -gi > 13.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 13.fasta < /dev/null @@@@ rm -f 13.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 14.fasta E=2000 V=20000 B=0 -gi > 14.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 14.fasta < /dev/null @@@@ rm -f 14.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 15.fasta E=2000 V=20000 B=0 -gi > 15.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 15.fasta < /dev/null @@@@ rm -f 15.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 16.fasta E=2000 V=20000 B=0 -gi > 16.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 16.fasta < /dev/null @@@@ rm -f 16.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 17.fasta E=2000 V=20000 B=0 -gi > 17.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 17.fasta < /dev/null @@@@ rm -f 17.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 18.fasta E=2000 V=20000 B=0 -gi > 18.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 18.fasta < /dev/null @@@@ rm -f 18.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 19.fasta E=2000 V=20000 B=0 -gi > 19.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 19.fasta < /dev/null @@@@ rm -f 19.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 20.fasta E=2000 V=20000 B=0 -gi > 20.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 20.fasta < /dev/null @@@@ rm -f 20.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 21.fasta E=2000 V=20000 B=0 -gi > 21.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 21.fasta < /dev/null @@@@ rm -f 21.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 22.fasta E=2000 V=20000 B=0 -gi > 22.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 22.fasta < /dev/null @@@@ rm -f 22.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 23.fasta E=2000 V=20000 B=0 -gi > 23.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 23.fasta < /dev/null @@@@ rm -f 23.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 24.fasta E=2000 V=20000 B=0 -gi > 24.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 24.fasta < /dev/null @@@@ rm -f 24.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 25.fasta E=2000 V=20000 B=0 -gi > 25.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 25.fasta < /dev/null @@@@ rm -f 25.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 26.fasta E=2000 V=20000 B=0 -gi > 26.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 26.fasta < /dev/null @@@@ rm -f 26.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 27.fasta E=2000 V=20000 B=0 -gi > 27.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 27.fasta < /dev/null @@@@ rm -f 27.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 28.fasta E=2000 V=20000 B=0 -gi > 28.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 28.fasta < /dev/null @@@@ rm -f 28.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 29.fasta E=2000 V=20000 B=0 -gi > 29.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 29.fasta < /dev/null @@@@ rm -f 29.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 30.fasta E=2000 V=20000 B=0 -gi > 30.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 30.fasta < /dev/null @@@@ rm -f 30.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 31.fasta E=2000 V=20000 B=0 -gi > 31.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 31.fasta < /dev/null @@@@ rm -f 31.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 32.fasta E=2000 V=20000 B=0 -gi > 32.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 32.fasta < /dev/null @@@@ rm -f 32.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 33.fasta E=2000 V=20000 B=0 -gi > 33.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 33.fasta < /dev/null @@@@ rm -f 33.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 34.fasta E=2000 V=20000 B=0 -gi > 34.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 34.fasta < /dev/null @@@@ rm -f 34.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 35.fasta E=2000 V=20000 B=0 -gi > 35.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 35.fasta < /dev/null @@@@ rm -f 35.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 36.fasta E=2000 V=20000 B=0 -gi > 36.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 36.fasta < /dev/null @@@@ rm -f 36.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 37.fasta E=2000 V=20000 B=0 -gi > 37.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 37.fasta < /dev/null @@@@ rm -f 37.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 38.fasta E=2000 V=20000 B=0 -gi > 38.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 38.fasta < /dev/null @@@@ rm -f 38.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 39.fasta E=2000 V=20000 B=0 -gi > 39.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 39.fasta < /dev/null @@@@ rm -f 39.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 40.fasta E=2000 V=20000 B=0 -gi > 40.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 40.fasta < /dev/null @@@@ rm -f 40.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 41.fasta E=2000 V=20000 B=0 -gi > 41.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 41.fasta < /dev/null @@@@ rm -f 41.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 42.fasta E=2000 V=20000 B=0 -gi > 42.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 42.fasta < /dev/null @@@@ rm -f 42.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 43.fasta E=2000 V=20000 B=0 -gi > 43.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 43.fasta < /dev/null @@@@ rm -f 43.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 44.fasta E=2000 V=20000 B=0 -gi > 44.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 44.fasta < /dev/null @@@@ rm -f 44.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 45.fasta E=2000 V=20000 B=0 -gi > 45.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 45.fasta < /dev/null @@@@ rm -f 45.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 46.fasta E=2000 V=20000 B=0 -gi > 46.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 46.fasta < /dev/null @@@@ rm -f 46.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 47.fasta E=2000 V=20000 B=0 -gi > 47.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 47.fasta < /dev/null @@@@ rm -f 47.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 48.fasta E=2000 V=20000 B=0 -gi > 48.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 48.fasta < /dev/null @@@@ rm -f 48.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 49.fasta E=2000 V=20000 B=0 -gi > 49.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 49.fasta < /dev/null @@@@ rm -f 49.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 50.fasta E=2000 V=20000 B=0 -gi > 50.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 50.fasta < /dev/null @@@@ rm -f 50.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 51.fasta E=2000 V=20000 B=0 -gi > 51.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 51.fasta < /dev/null @@@@ rm -f 51.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 52.fasta E=2000 V=20000 B=0 -gi > 52.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 52.fasta < /dev/null @@@@ rm -f 52.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 53.fasta E=2000 V=20000 B=0 -gi > 53.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 53.fasta < /dev/null @@@@ rm -f 53.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 54.fasta E=2000 V=20000 B=0 -gi > 54.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 54.fasta < /dev/null @@@@ rm -f 54.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 55.fasta E=2000 V=20000 B=0 -gi > 55.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 55.fasta < /dev/null @@@@ rm -f 55.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 56.fasta E=2000 V=20000 B=0 -gi > 56.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 56.fasta < /dev/null @@@@ rm -f 56.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 57.fasta E=2000 V=20000 B=0 -gi > 57.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 57.fasta < /dev/null @@@@ rm -f 57.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 58.fasta E=2000 V=20000 B=0 -gi > 58.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 58.fasta < /dev/null @@@@ rm -f 58.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 59.fasta E=2000 V=20000 B=0 -gi > 59.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 59.fasta < /dev/null @@@@ rm -f 59.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 60.fasta E=2000 V=20000 B=0 -gi > 60.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 60.fasta < /dev/null @@@@ rm -f 60.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 61.fasta E=2000 V=20000 B=0 -gi > 61.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 61.fasta < /dev/null @@@@ rm -f 61.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 62.fasta E=2000 V=20000 B=0 -gi > 62.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 62.fasta < /dev/null @@@@ rm -f 62.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 63.fasta E=2000 V=20000 B=0 -gi > 63.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 63.fasta < /dev/null @@@@ rm -f 63.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 64.fasta E=2000 V=20000 B=0 -gi > 64.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 64.fasta < /dev/null @@@@ rm -f 64.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 65.fasta E=2000 V=20000 B=0 -gi > 65.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 65.fasta < /dev/null @@@@ rm -f 65.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 66.fasta E=2000 V=20000 B=0 -gi > 66.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 66.fasta < /dev/null @@@@ rm -f 66.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 67.fasta E=2000 V=20000 B=0 -gi > 67.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 67.fasta < /dev/null @@@@ rm -f 67.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 68.fasta E=2000 V=20000 B=0 -gi > 68.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 68.fasta < /dev/null @@@@ rm -f 68.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 69.fasta E=2000 V=20000 B=0 -gi > 69.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 69.fasta < /dev/null @@@@ rm -f 69.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 70.fasta E=2000 V=20000 B=0 -gi > 70.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 70.fasta < /dev/null @@@@ rm -f 70.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 71.fasta E=2000 V=20000 B=0 -gi > 71.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 71.fasta < /dev/null @@@@ rm -f 71.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 72.fasta E=2000 V=20000 B=0 -gi > 72.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 72.fasta < /dev/null @@@@ rm -f 72.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 73.fasta E=2000 V=20000 B=0 -gi > 73.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 73.fasta < /dev/null @@@@ rm -f 73.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 74.fasta E=2000 V=20000 B=0 -gi > 74.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 74.fasta < /dev/null @@@@ rm -f 74.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 75.fasta E=2000 V=20000 B=0 -gi > 75.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 75.fasta < /dev/null @@@@ rm -f 75.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 76.fasta E=2000 V=20000 B=0 -gi > 76.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 76.fasta < /dev/null @@@@ rm -f 76.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 77.fasta E=2000 V=20000 B=0 -gi > 77.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 77.fasta < /dev/null @@@@ rm -f 77.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 78.fasta E=2000 V=20000 B=0 -gi > 78.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 78.fasta < /dev/null @@@@ rm -f 78.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 79.fasta E=2000 V=20000 B=0 -gi > 79.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 79.fasta < /dev/null @@@@ rm -f 79.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 80.fasta E=2000 V=20000 B=0 -gi > 80.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 80.fasta < /dev/null @@@@ rm -f 80.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 81.fasta E=2000 V=20000 B=0 -gi > 81.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 81.fasta < /dev/null @@@@ rm -f 81.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 82.fasta E=2000 V=20000 B=0 -gi > 82.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 82.fasta < /dev/null @@@@ rm -f 82.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 83.fasta E=2000 V=20000 B=0 -gi > 83.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 83.fasta < /dev/null @@@@ rm -f 83.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 84.fasta E=2000 V=20000 B=0 -gi > 84.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 84.fasta < /dev/null @@@@ rm -f 84.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 85.fasta E=2000 V=20000 B=0 -gi > 85.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 85.fasta < /dev/null @@@@ rm -f 85.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 86.fasta E=2000 V=20000 B=0 -gi > 86.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 86.fasta < /dev/null @@@@ rm -f 86.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 87.fasta E=2000 V=20000 B=0 -gi > 87.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 87.fasta < /dev/null @@@@ rm -f 87.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 88.fasta E=2000 V=20000 B=0 -gi > 88.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 88.fasta < /dev/null @@@@ rm -f 88.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 89.fasta E=2000 V=20000 B=0 -gi > 89.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 89.fasta < /dev/null @@@@ rm -f 89.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 90.fasta E=2000 V=20000 B=0 -gi > 90.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 90.fasta < /dev/null @@@@ rm -f 90.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 91.fasta E=2000 V=20000 B=0 -gi > 91.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 91.fasta < /dev/null @@@@ rm -f 91.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 92.fasta E=2000 V=20000 B=0 -gi > 92.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 92.fasta < /dev/null @@@@ rm -f 92.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 93.fasta E=2000 V=20000 B=0 -gi > 93.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 93.fasta < /dev/null @@@@ rm -f 93.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 94.fasta E=2000 V=20000 B=0 -gi > 94.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 94.fasta < /dev/null @@@@ rm -f 94.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 95.fasta E=2000 V=20000 B=0 -gi > 95.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 95.fasta < /dev/null @@@@ rm -f 95.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 96.fasta E=2000 V=20000 B=0 -gi > 96.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 96.fasta < /dev/null @@@@ rm -f 96.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 97.fasta E=2000 V=20000 B=0 -gi > 97.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 97.fasta < /dev/null @@@@ rm -f 97.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 98.fasta E=2000 V=20000 B=0 -gi > 98.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 98.fasta < /dev/null @@@@ rm -f 98.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 99.fasta E=2000 V=20000 B=0 -gi > 99.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 99.fasta < /dev/null @@@@ rm -f 99.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 100.fasta E=2000 V=20000 B=0 -gi > 100.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 100.fasta < /dev/null @@@@ rm -f 100.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 101.fasta E=2000 V=20000 B=0 -gi > 101.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 101.fasta < /dev/null @@@@ rm -f 101.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 102.fasta E=2000 V=20000 B=0 -gi > 102.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 102.fasta < /dev/null @@@@ rm -f 102.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 103.fasta E=2000 V=20000 B=0 -gi > 103.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 103.fasta < /dev/null @@@@ rm -f 103.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 104.fasta E=2000 V=20000 B=0 -gi > 104.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 104.fasta < /dev/null @@@@ rm -f 104.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 105.fasta E=2000 V=20000 B=0 -gi > 105.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 105.fasta < /dev/null @@@@ rm -f 105.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 106.fasta E=2000 V=20000 B=0 -gi > 106.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 106.fasta < /dev/null @@@@ rm -f 106.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 107.fasta E=2000 V=20000 B=0 -gi > 107.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 107.fasta < /dev/null @@@@ rm -f 107.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 108.fasta E=2000 V=20000 B=0 -gi > 108.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 108.fasta < /dev/null @@@@ rm -f 108.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 109.fasta E=2000 V=20000 B=0 -gi > 109.fasta-blast.out WARNING: THE QUERY SEQUENCE APPEARS TO BE NUCLEIC ACID WHEN A PROTEIN SEQUENCE IS EXPECTED BY THIS PROGRAM. Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 109.fasta < /dev/null @@@@ rm -f 109.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 110.fasta E=2000 V=20000 B=0 -gi > 110.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 110.fasta < /dev/null @@@@ rm -f 110.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 111.fasta E=2000 V=20000 B=0 -gi > 111.fasta-blast.out Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 111.fasta < /dev/null @@@@ rm -f 111.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 112.fasta E=2000 V=20000 B=0 -gi > 112.fasta-blast.out WARNING: THE QUERY SEQUENCE APPEARS TO BE NUCLEIC ACID WHEN A PROTEIN SEQUENCE IS EXPECTED BY THIS PROGRAM. Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 112.fasta < /dev/null @@@@ rm -f 112.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 113.fasta E=2000 V=20000 B=0 -gi > 113.fasta-blast.out WARNING: THE QUERY SEQUENCE APPEARS TO BE NUCLEIC ACID WHEN A PROTEIN SEQUENCE IS EXPECTED BY THIS PROGRAM. Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 113.fasta < /dev/null @@@@ rm -f 113.fasta-blast.out < /dev/null @@@@ /projects/compbio/bin/wu-blastp /projects/compbio/data/nrp/nr 114.fasta E=2000 V=20000 B=0 -gi > 114.fasta-blast.out WARNING: THE QUERY SEQUENCE APPEARS TO BE NUCLEIC ACID WHEN A PROTEIN SEQUENCE IS EXPECTED BY THIS PROGRAM. Searched 509169 sequences # parsing wu-blastp output @@@@ rm -f 114.fasta < /dev/null @@@@ rm -f 114.fasta-blast.out < /dev/null # Extracting hits in FASTA format from /projects/compbio/data/nrp/nr @@@@ rm -rf /projects/compbio/tmp/blast-prefilter-beta-22590 < /dev/null @@@@ modelfromalign unused -alignfile m0.a2m \ -constraints_from_align 1 -constraints_out m0.cst SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (119 sequences, 342 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file m0.a2m (119 sequences, 342 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 509169 \ -simple_threshold -19.4431201605963 -Emax 0.1 \ -adpstyle 1 \ -align_short 0 -mdEmax 0.1\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -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(23): Reading MODEL -- Model from alignment file m0.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) ....................... Average NLL-Simple NULL score: -10.933824 Database has 22071 sequences with 4335725 residues. @@@@ sortseq tmp_1-a-sort -alignfile tmp_1-a.mult \ -NLLfile tmp_1-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_1-a.mult (133 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_1-a.mstat Writing sequence output to tmp_1-a-sort.a2m. @@@@ cat m0.a2m tmp_1-a-sort.a2m > tmp_1-a.train.seq @@@@ cat m0.cst tmp_1-a-md.cst > tmp_1-a.train.cst # About to count sequences in tmp_1-a.train.seq # num_seqs=252 nll_thresh=-15.4431201605962 frac_id=0.718867457172798 @@@@ uniqueseq thinned_tmp -alignfile tmp_1-a.train.seq -a protein \ -percent_id 0.718867457172798 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_1-a.train.seq (252 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 6 (of 252) duplicate sequences with differing IDs Dropping 6 (of 252) duplicate sequences with identical IDs Dropping 167 (of 252) sequences with > 71.9% id 64 sequences left after dropping 188 of 252 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_1-a.train.seq \ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_1-a.train.seq (64 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_1-b -insert 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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_1-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/gap1.5.regularizer -sequence_weights tmp_1-a.w -constraints tmp_1-a.train.cst Reading parameter file tmp_1-a.mod tmp_1-a.mod(23): Reading MODEL -- Model from alignment file m0.a2m Command line option(48): internal_weight has already been set. Using 0. 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: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -965.47 111.64 -300.48 235.80 18 0 343 @@@@ hmmscore tmp_1-b -i tmp_1-b.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 509169 \ -db m0.a2m -db tmp_1-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -19.4431201605963 -Emax 0.1 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 0.1 -constraints tmp_1-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.cst Reading parameter file tmp_1-b.mod tmp_1-b.mod(20): Reading MODEL -- Final model for run tmp_1-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -488.565277 Database has 253 sequences with 88162 residues. @@@@ cp -f tmp_1-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.a2m # About to count sequences in prefilter_2.fa @@@@ modelfromalign tmp_2-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.a2m \ -insert /projects/compbio/lib/stiff-gap5.regularizer \ -aweight_bits 0.7\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.cst -constraints_out tmp_2-a.cst Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.a2m (252 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_2-a -i tmp_2-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 509169 \ -simple_threshold -17.1405333000143 -Emax 1 \ -adpstyle 1 \ -align_short 0 -mdEmax 1\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_2.fa -constraints tmp_2-a.cst -constraints_out tmp_2-a-md.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) ....................... Average NLL-Simple NULL score: -13.063528 Database has 22071 sequences with 4335725 residues. @@@@ sortseq tmp_2-a-sort -alignfile tmp_2-a.mult \ -NLLfile tmp_2-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_2-a.mult (137 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_2-a.mstat Writing sequence output to tmp_2-a-sort.a2m. @@@@ cat m0.a2m tmp_2-a-sort.a2m > tmp_2-a.train.seq @@@@ cat m0.cst tmp_2-a-md.cst > tmp_2-a.train.cst # About to count sequences in tmp_2-a.train.seq # num_seqs=256 nll_thresh=-13.1405333000143 frac_id=0.700464191993594 @@@@ uniqueseq thinned_tmp -alignfile tmp_2-a.train.seq -a protein \ -percent_id 0.700464191993594 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_2-a.train.seq (256 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 8 (of 256) duplicate sequences with differing IDs Dropping 8 (of 256) duplicate sequences with identical IDs Dropping 174 (of 256) sequences with > 70.0% id 64 sequences left after dropping 192 of 256 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_2-a.train.seq \ -aweight_bits 0.7\ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_2-a.train.seq (64 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_2-b -insert tmp_2-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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_2-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/stiff-gap5.regularizer -sequence_weights tmp_2-a.w -constraints tmp_2-a.train.cst Reading parameter file tmp_2-a.mod tmp_2-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_1.a2m Command line option(48): internal_weight has already been set. Using 0. Reading parameter file /projects/compbio/lib/stiff-gap5.regularizer /projects/compbio/lib/stiff-gap5.regularizer(1): Reading REGULARIZER: gap5. stiff regularizer, gaps averge 5, matches average 10 SAM: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -964.24 31.18 -241.97 165.76 20 0 343 @@@@ hmmscore tmp_2-b -i tmp_2-b.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 509169 \ -db m0.a2m -db tmp_2-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -17.1405333000143 -Emax 1 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 1 -constraints tmp_2-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.cst Reading parameter file tmp_2-b.mod tmp_2-b.mod(20): Reading MODEL -- Final model for run tmp_2-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -420.482635 Database has 273 sequences with 100666 residues. @@@@ cp -f tmp_2-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.a2m # About to count sequences in prefilter_3.fa @@@@ modelfromalign tmp_3-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.6\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.cst -constraints_out tmp_3-a.cst 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.a2m (256 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_3-a -i tmp_3-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 509169 \ -simple_threshold -14.8379305309692 -Emax 10 \ -adpstyle 1 \ -align_short 0 -mdEmax 10\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_3.fa -constraints tmp_3-a.cst -constraints_out tmp_3-a-md.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) ....................... Average NLL-Simple NULL score: -10.562375 Database has 22071 sequences with 4335725 residues. @@@@ sortseq tmp_3-a-sort -alignfile tmp_3-a.mult \ -NLLfile tmp_3-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_3-a.mult (141 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_3-a.mstat Writing sequence output to tmp_3-a-sort.a2m. @@@@ cat m0.a2m tmp_3-a-sort.a2m > tmp_3-a.train.seq @@@@ cat m0.cst tmp_3-a-md.cst > tmp_3-a.train.cst # About to count sequences in tmp_3-a.train.seq # num_seqs=260 nll_thresh=-10.8379305309692 frac_id=0.682182141314692 @@@@ uniqueseq thinned_tmp -alignfile tmp_3-a.train.seq -a protein \ -percent_id 0.682182141314692 -a2mdots 0 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file tmp_3-a.train.seq (260 sequences, 342 columns) as A2M alignment. Writing sequence output to thinned_tmp.a2m. Dropping 9 (of 260) duplicate sequences with differing IDs Dropping 9 (of 260) duplicate sequences with identical IDs Dropping 177 (of 260) sequences with > 68.2% id 63 sequences left after dropping 197 of 260 sequences. @@@@ modelfromalign junk_for_weights \ -alignfile tmp_3-a.train.seq \ -aweight_bits 0.6\ -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 SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file tmp_3-a.train.seq (63 sequences, 342 columns) as A2M alignment. @@@@ buildmodel tmp_3-b -insert tmp_3-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\ -modellength 0 \ -internal_weight 0 \ -anneal_length 2 \ -many_files 1 \ -Nseq 20000\ -nsurgery 0 \ -fracinsert 0.2 \ -cutinsert 0.25 -cutmatch 0.2 -initial_noise 0.0001 -anneal_noise 0.000001 \ -internal_weight 0 \ -train tmp_3-a.train.seq \ -nmodels 1\ -insert /projects/compbio/lib/fssp-trained.regularizer -sequence_weights tmp_3-a.w -constraints tmp_3-a.train.cst Reading parameter file tmp_3-a.mod tmp_3-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_2.a2m Command line option(48): internal_weight has already been set. Using 0. 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: buildmodel v3.1b (February 24, 1999) compiled 04/18/00_11:43:59 -965.30 -0.30 -278.41 215.51 16 0 343 @@@@ hmmscore tmp_3-b -i tmp_3-b.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 509169 \ -db m0.a2m -db tmp_3-a.sel \ -select_score 4 \ -select_seq 4 \ -simple_threshold -14.8379305309692 -Emax 10 \ -select_mdalign 4 -select_md 4 \ -adpstyle 1 \ -Motifcutoff 0.0584795321637427 \ -align_short 5 -mdEmax 10 -constraints tmp_3-a.train.cst -constraints_out /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_3.cst Reading parameter file tmp_3-b.mod tmp_3-b.mod(20): Reading MODEL -- Final model for run tmp_3-b SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -454.988403 Database has 261 sequences with 94830 residues. @@@@ cp -f tmp_3-b.mult /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_3.a2m @@@@ modelfromalign tmp_4-a -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_3.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -aweight_bits 0.6\ -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 /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_3.cst -constraints_out tmp_4-a.cst 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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_3.a2m (261 sequences, 342 columns) as A2M alignment. @@@@ hmmscore tmp_4-a -i tmp_4-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 509169 \ -simple_threshold -14.8379305309692 -Emax 10 \ -adpstyle 5 \ -align_short 0 -mdEmax 10\ -select_score 4 \ -select_seq 4 \ -select_mdalign 4 -select_md 4 -Motifcutoff 0.0584795321637427 -db prefilter_3.fa -constraints tmp_4-a.cst -constraints_out tmp_4-a-md.cst Reading parameter file tmp_4-a.mod tmp_4-a.mod(23): Reading MODEL -- Model from alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k_3.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) ....................... Average NLL-Simple NULL score: -10.573856 Database has 22071 sequences with 4335725 residues. @@@@ sortseq tmp_4-a-sort -alignfile tmp_4-a.mult \ -NLLfile tmp_4-a.mstat -a2mdots 0 SAM: sortseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:38 Reading alignment file tmp_4-a.mult (126 sequences, 342 columns) as A2M alignment. Reading scores from file tmp_4-a.mstat Writing sequence output to tmp_4-a-sort.a2m. @@@@ cat m0.a2m tmp_4-a-sort.a2m > tmp_4-a.train.seq @@@@ cat m0.cst tmp_4-a-md.cst > tmp_4-a.train.cst @@@@ cp tmp_4-a.train.seq /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k.a2m @@@@ cp tmp_4-a.train.cst /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k.cst @@@@ rm -rf /projects/compbio/tmp/target2k-beta-3276 < /dev/null gzip -9f T0100.remote-t2k.a2m /projects/compbio/experiments/models.97/scripts99/score-target -alignment T0100.remote-t2k.a2m.gz -build w0.5 \ -db /projects/compbio/data/pdb/all-protein \ -Emax 40.0 \ -viterbi 0 -sw_score 2 \ -output T0100.remote-t2k-w0.5-pdb.rdb PATH=.:/projects/compbio/experiments/models.97/scripts99:/projects/compbio/bin:/projects/compbio/bin/alpha:/projects/compbio/bin/hmmscripts:/projects/compbio/bin/scripts:/sbin:/usr/sbin:/bin:/usr/bin:/usr/local/gnu/bin:/usr/local/share/request/bin:/usr/local/bin @@@@ mkdir /projects/compbio/tmp/score-target-11698 @@@@ mkdir /projects/compbio/tmp/score-target-11698/for-scorescript @@@@ /projects/compbio/experiments/models.97/scripts99/score-mods-vs-seqs.pl -root_tmp /projects/compbio/tmp/score-target-11698/for-scorescript -a2msfile /projects/compbio/tmp/score-target-11698/score-target.a2m \ -buildscript /projects/compbio/bin/scripts/w0.5 -seqfile /projects/compbio/data/pdb/all-protein -Emax 40.0 -viterbi 0 \ -sw_score 2 -output /projects/compbio/tmp/score-target-11698/score-target.op @@@@ chgrp protein /projects/compbio/tmp/score-target-11698/for-scorescript/split-tmp @@@@ chgrp protein /projects/compbio/tmp/score-target-11698/for-scorescript/split-tmp @@@@ /projects/compbio/bin/scripts/w0.5 /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k.a2m.gz /projects/compbio/tmp/score-target-11698/for-scorescript/split-tmp/beta-22068/T0100.remote-t2k.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2646 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2646/tmp -alignfile /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file /export/projects/compbio/experiments/casp4/t100/T0100.remote-t2k.a2m.gz (245 sequences, 342 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2646/tmp.a2m. Dropping 7 (of 245) duplicate sequences with differing IDs Dropping 7 (of 245) duplicate sequences with identical IDs Dropping 87 (of 245) sequences with > 80.0% id 80 sequences left after dropping 165 of 245 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2646/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2646/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 v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2646/tmp.a2m (80 sequences, 342 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2646/tmp.mod /projects/compbio/tmp/score-target-11698/for-scorescript/split-tmp/beta-22068/T0100.remote-t2k.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2646 tmp.script echo ReadA2M T0100.t2k.a2m.gz >> tmp.script echo PrintPrediction T0100.t2k.2d 3670-4530-6947 >> tmp.script echo PrintPredictionFasta T0100.t2k.2d.seq >> tmp.script echo PrintRDB T0100.t2k.2d.rdb >> tmp.script predict-2nd < tmp.script # command:# Neural network set to overrep-2500-IDaa13-5-10-7-10-5-10-11-ehl2-seeded9-stride-trained.net # command:# Reading A2M format from T0100.t2k.a2m.gz # Using SequenceWeight EntropyWeight(1.4, 10) # Using regularizer /projects/compbio/lib/recode3.20comp for sequence weight regularizer. # T0100.t2k.a2m with 119 sequences, total weight= 30.0563 avg weight= 0.252574 46 iterations Regularizing alignment for T0100.t2k.a2m.gz # After reading T0100.t2k.a2m.gz, have 342 columns in 1 chains # command:# Initializing Gain for FinalLayer # Initializing Gain for ordering_layer # Initializing Gain for SecondLayer # Initializing Gain for FirstLayer # Network initialization done # Printing prediction to T0100.t2k.2d # command:# Network initialization done # Printing prediction in FASTA format to T0100.t2k.2d.seq # command:# Network initialization done # Printing prediction to T0100.t2k.2d.rdb # command:rm tmp.script make: `T0100.t2k.2d' is up to date.