Params: ./cmzasha --no-stderr --filter 150 16 Rfam/cm/RF00043.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00043_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin Build: release Host: boudin.cs.washington.edu pid: 9535 ----cmFile: Rfam/cm/RF00043.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/phg.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----sequence: #17966,sp|AF325537.2|AF325537 Acidithiobacillus caldus plasmid pTC-F14 replicon, complete sequence. ----isReversed: 0 ----hitSequence: CGGCGCGAGCCGGAGUGUCAGUCCCCGGCAGCGCCUAACCACGCCAGUUCUGGAAAGGAGAACAGCAUGGCUUU hit 0 : 5765 5838 (fwd) 39.39 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 CGGCGC++G:CGG:G++U++GUC:CCG:CAGCGCCUAACCAC++++:::CUG:AAA:GAG 5765 CGGCGCGAGCCGGAGUGUCAGUCCCCGGCAGCGCCUAACCACGCCAGUUCUGGAAAGGAG 5824 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 :::A+C AUGGCU++ 5825 AACAGC--AUGGCUUU 5838 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #6851,sp|AY043298.1|AY043298 Aeromonas salmonicida subsp. salmonicida plasmid pRAS3.1, complete sequence. ----isReversed: 1 ----hitSequence: CGGCGCGGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAGAACAGCAUGGCUUU hit 1 : 7823 7750 (rev) 16.12 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 CGGCGC+ : GG: + G+ :CC : AGCGCCUAACCA+ A+C:::CU CA AGGAG 4029 CGGCGCGGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAG 4088 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 :::A+C AUGGCU++ 4089 AACAGC--AUGGCUUU 4102 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #6852,sp|AY043299.1|AY043299 Aeromonas salmonicida plasmid pRAS3.2, complete sequence. ----isReversed: 1 ----hitSequence: CGGCGCGGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAGAACAGCAUGGCUUU hit 2 : 7801 7728 (rev) 16.12 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 CGGCGC+ : GG: + G+ :CC : AGCGCCUAACCA+ A+C:::CU CA AGGAG 4023 CGGCGCGGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAG 4082 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 :::A+C AUGGCU++ 4083 AACAGC--AUGGCUUU 4096 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #41041,sp|Z78058.1|BSPCAC Bacteria sp. plasmid pIE1024 (partial). ----isReversed: 0 ----hitSequence: UAGCGCUUAUGGGGUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAGGCAAUCAAUGGCUAC hit 3 : 1759 1831 (fwd) 34.00 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 :GCGC U:: GGGGU+GUG+CCCCG::AGCGC:UAACCACCAACUGCCUGCAAAGGAG 1759 UAGCGCUUAU--GGGGUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAG 1816 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 GCAAUC AAUGGCUAC 1817 GCAAUC-AAUGGCUAC 1831 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----sequence: #47748,sp|Y19120.1|DN1Y19120 Dichelobacter nodosus plasmid DN1 ----isReversed: 0 ----hitSequence: CGGCGCAUGGCGGGGCAUCCCCGCCAGCGCUUGACCAUCAACCGCCUGCAAAGGAGGCAAACCAAUGGCUAC hit 4 : 3371 3442 (fwd) 36.79 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 C:GCGCAUGGCGGGG UCCCCGCCAGCGC:U+ACCA+CAAC:GCCUGCAAAGGAG 3371 CGGCGCAUGGCGGGGCA----UCCCCGCCAGCGCUUGACCAUCAACCGCCUGCAAAGGAG 3426 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 GC:A+CCAAUGGCUAC 3427 GCAAACCAAUGGCUAC 3442 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #825,sp|Z47410.1|ECINCQAAT E.coli IncQ plasmid aadB gene for aminoglycoside adenylyltransferase. ----isReversed: 0 ----hitSequence: CGGCGCAGGGCGGGGGUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAGGCAAUCAAUGGCUAC hit 5 : 1220 1294 (fwd) 47.12 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 CGGCGCA GGCGGGGGU+GUG+CCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAG 1220 CGGCGCAGGGCGGGGGUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAG 1279 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 GCAAUC AAUGGCUAC 1280 GCAAUC-AAUGGCUAC 1294 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #45465,sp|AJ271879.1|UEU271879 Uncultured eubacterium plasmid pIE1130 DNA for repA gene, repC gene, repB gene, mobA gene, mobB gene, mobC gene, cac gene, catI ----isReversed: 0 ----hitSequence: CGGCGCAGGGCGGGGGUGGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGAACAGGAGGCAAUCAUGGCUAC hit 6 : 3249 3322 (fwd) 42.53 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 CGGCGCA GGCGGGGGU GUG+CCCCGCCAGCGCCUAACCACCAACUGCCUG:A A:GAG 3249 CGGCGCAGGGCGGGGGUGGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGAACAGGAG 3308 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 GCAAUC AUGGCUAC 3309 GCAAUC--AUGGCUAC 3322 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----sequence: #45782,sp|AJ293027.1|UEU293027 Uncultured eubacterium pIE1115 plasmid pIE1115, complete sequence ----isReversed: 0 ----hitSequence: CGGCGCAUGGCGGGGAUGCCCCGCCAGCGCCUGACCAUCAACCGCCUGCAAAGGAGGCAAACCAAUGGCUAC hit 7 : 2887 2958 (fwd) 38.39 bits :<<<<<--<<<<<<<_______>>>>>>>->>>>>---<<<-----<<<<<-<___>->> 1 CggcgcauggcggggguuguGuccccgccAgcgccUAAccaCcaacugccuGcAAAgGag 60 CGGCGCAUGGCGGGG U CCCCGCCAGCGCCU+ACCA+CAAC:GCCUGCAAAGGAG 2887 CGGCGCAUGGCGGGGAU----GCCCCGCCAGCGCCUGACCAUCAACCGCCUGCAAAGGAG 2942 >>>------>>>:::: 61 gcaAuCcAAuggCUac 76 GC:A+CCAAUGGCUAC 2943 GCAAACCAAUGGCUAC 2958 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum08.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum09.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum26.dat.fasta.gz done 1.65905e+10 nucs (frac lets thru so far=8.23361e-08, 2d-fracLetsThru=4.70392e-08). Filter report: done 1.65905e+10 nucs (frac lets thru so far=8.23361e-08, 2d-fracLetsThru=4.70392e-08). done 1.65905e+10 nucs (frac lets thru so far=8.23361e-08, 2d-fracLetsThru=4.70392e-08). CPU time: 214315.33u 285.57s 59:36:40.89 Elapsed: 59:37:03