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U AE ,3,0ޡ<3ɐ EU;WD~MM]; ~EuU;fEMAM];_D: U ]AǤ,0<3ɐ EE;GD~UUM;~]];_ Ӝ=@tɟh@rh@\ɟɟPC\e[^_vUlWVS=@t!ɟhdrh@˥\ɟɟP\ɟ1EHH9KU;zD1 uDDɬ G;~D~1E;xH}.1uDDɬ G;~H|}OH9wUPɯu9ɯu]9uVܔ(ލĔEĸP11VU9}u1M*h ފUnj,8ފEUBU@,ފUBŤ(ޘ,8ޡC<8ɫ ;ZH|u]KH9lEu9ut&}UцPG}ɯu9ɯu]919H}<}EXPM} R},ޡ1F<EU;ZH}]M9MuEUE,:h ފUnjU,ފUBjt&MŔEM,:h ފUnjM,ފEUMDM@,ފUBMŤ(ޘUM,ޡC<ɡ M;ZH u]CH9塜uu}9g=G{EEU;BeɟMQɟhqh@/YɟPYɟɟPzXɟɟ]ɥu0ɟhqh@XɟPˮYɟɟP UǨ] U]AǤ,0<3ɐ GE;xD~UUMŨ];~uu};w 鲜=Ct{1UBH9}ot&1NM9}Nm1U },ފ,mފޡ, ޡC< ɡ ;_H|uUBH9|=B}1M;qH}s^]E;xDQmȼ U]ɯ,ފ,mފޡ, ޡG< ɡ ;{D~u};wH|e[^_UWVS=@t!ɟhrh@XTɟɟP˨Sɟ1{1OU;ZD.1uܯDDɬ C;^D~1E;XH}41uDDɬ C;^H|E;xHyUz Jl]Cp@,С<;]W}L7lD7p@,<L7l}7@,Cɐ<;]~=Ct[1UBH9}O1^]9}61U ],ފ, ޡG< ɡ ;{H|u}GH9|=Bt`1TVU};_D> t&U},ފ, ޡC< ɡ ;_D~uE;pH|=@tɟhrh@>RɟɟPQe[^_U WVS]=@t!ɟhsh@RɟɟPUQɟ1;sH}wv~;KD. DDɬ A;KD~1;KH}+1 DDɬ A;KH|;sH|=@tɟh@sh@YQɟɟP˂Pe[^_U,WVSu=C1w9OM<ubֳ~ ⋤(ޡɿ IuĔEĸu19}'1ܟ ,<Ɉ A;NH|}VH9|=Bш1;~H&9WU<Ӫ;^D6 (, ޡC< ,ɡ ޡ;^D~ĔEĸuӪ;^D) ܺ,< ɡ C;^D~};~HO[^_U WVSu=@t!ɟhcsh˩OɟɟP˛Nɟ1;FH}Kt&NDx9((, MEފCND9~;FH|=@tɟhsh-OɟɟPNe[^_UWVS} ֿ~ =ֿ v'Uⲡ ⠡)[⬡))⬡  ⬡C)yšɜ @ Ny@ Uⲡ ⠡)[⬡))⬡  ⬡C)yš  zOⲡ⠡)[)))))) ))⬡) y š  U⠡)@ ) @ ֊ š  s]EsĔEus[^_US=t Ɉ;u[]U]US[ň4UˣN[BDGPQVabcfhptuvPlease read the README file for help set option u: assume input is ds DNA and compute both strands independently from each otherset option e: assume input is ds DNA and compute both strands conjointlyset option t: use tying of emission probabilities as specified in the model file (only for Baum Welch)set option p: use tying of emission probabilities for pairs of complementary states as specified in the model file (only for Baum Welch)set option G: generate sequenceset option B: Baum-Welch trainingset option D: Posterior Decodingset option Q: Viterbi Probability and Decodingset option V: Viterbi Learningset option P: FB-ProbabilityUnrecognized option: Error:missing filename after option -s Warning: filename too long max = 100 char Error:missing filename after option -m Error:missing number after option -g Error:missing number after option -d Error:missing number after option -n Error:missing number after option -i Error:missing number after option -j Error:missing number after option -k set storeseqs Error:missing number after option -l Error:missing number after option -w set option w: weight for pseudocounts = +d => set write domain parsing +l => set write list of coiled-coil probabilities +m => set write compact list of probabilities +s => set write probabilities for each state (not for PSSM) +S => set write protein sequence Error:missing number after option +c Unrecognized option +Unrecognized option: Set CutoffForWriting to Using default CutoffForWriting = No model file was specified, will use default: INPUT/R1.model INPUT/R1.model No sequence file was specified, will use default: SEQUENCES/seqFile SEQUENCES/seqFile Sorry: the ds option is only available for BaumWelch 8{Gzt?{Gz????Gz?@@@@@@@@@@@ @@@@@@@@@@@@@@@ @@@@@@@@`@@@@`@@@0@@@@@@@P, WAS TRUNCATED IS LONGER THAN SEQUENCE NB WriteWarning concluded %c starting WriteSeq >SEQUENCE NB %s ## %d * * %s ## %d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . NUMBER PREDICTED COILED-COIL DOMAINS WITH THRESHOLD %3.1f : %d %2d. from %d to %d (length = %d) with max = %3.1f **************************************************************************************************************************************************************** B>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ in Sequence } at Position =Warning: Non expected letter { Sequence too long, sequence: starting FBmainr could not open the file for the sequences with address wFBprob could not open the file FBprob for writing FBpostprob could not open the file FBpostprob for writing ReadSeq done %s read seq-Nb = %d name = %s name = >>read seq-Nb processing seq-Nb #ln(FB-P)=%6.15f sequences, one lineOne point.$ processed seq-nb= Failed in malloc seqsmem in BWmain Failed in malloc seqsin BWmain Failed in malloc seqsLen in BWmain The nb of sequences and their maximal length are required with option -kwBWprot could not open the file BWprot for writing 1. BEFORE BAUM-WELCH, INITIAL MODEL r could not open the file for the sequences with address AFTER ITERATION NB=%d AFTER LAST ITERATION BWmaindsDNAĜ?start rcseqEnd CheckStop at iteration logLik of the learning set of sequences logLik of sequence set= difftotLogLik of sequence set= prevtotLogLik of sequence set= origtotLogLik of sequence set= iterationNb of sequence set= ORIG logLik=%g PREV logLik=%g PRES logLik=%g DIFF logLik=%g wGenSeqs could not open the file GenSeqs for writing Generate a random sequence: Enter seed (type long int, for ex. 35 ): set seed to: set negative seed to: >random_seq.>random_seq.%d VitLearnMainwVitLEARNdecprob could not open the file Vitdecprob for writing Failed in malloc seqsmem in VitLearnMain Failed in malloc seqsin VitLearnMain Failed in malloc seqsLen in VitLearnMain The nb of sequences and their maximal length are required with option -kVLprot could not open the file VLprot for writing 1. BEFORE VITERBI-LEARNING, INITIAL MODEL r could not open the file for the sequences with address AFTER ITERATION NB=%d AFTER LAST ITERATION at iteration logLik of the learning set of sequences logLik of sequence set= difftotLogLik of sequence set= prevtotLogLik of sequence set= origtotLogLik of sequence set= iterationNb of sequence set= ORIG logLik=%g PREV logLik=%g PRES logLik=%g DIFF logLik=%g w Vitprob could not open the file Vitprob for writing Vitdecprob could not open the file Vitdecprob for writing r could not open the file for the sequences with address read seq-Nb = %d name = %s %s # ln(Vit-P)=%g %s PlatformMain, modus = r could not open the model filecalled: ERROR finished ReadModel modus 0: FB-probability FBmain=>PlatformMain modus 1: Generation of (pseudo)random sequences modus 2: BaumWelch Training modus 3: Posterior Decoding modus 4: Viterbi Probability modus 5: Viterbi Learning. THIS IMPLEMENTATION HAS NOT BEEN TESTED yet. default: Posterior Decoding s0R starting ReadModel Statecompl_emtie_em Alphabet letters alphabet with maxnbtiesingroup = nbstates = tie_em = compl_em = call AssignMemory call ReadModelFB wModel could not open the file Model for writing ending ReadModel starting ModelFB::ReadModelFB, with: nbLetters= nbStates= maxSeqLength= Alphabet with options -u, -v and -p the Alphabet must be ACGT in this order with options -u, -v and -p the Alphabet must be of 4 letters ACGT in this orderState %sENDBEGINE:T:could not be identified as a valid state in the "T:" section of state error: the state NULLMODEL:fix_tr in the "fixed trans:" section could not be identified as a valid statetie_em in a "tie_em:" line could not be identified as a valid statecompl_em in a "compl_em:" line could not be identified as a valid state error: found more than two states in a "compl_em:" linefix_em in the "fixed emiss:" section could not be identified as a valid state ending ModelFB::ReadModelFB starting ModelFB::WriteModelFBAlphabet: %c Alphabet: ################################################ State %s E: %g Warning: emission probabilities of state %s do not sum up to 1 but to %2.15g T: %s %g END 0 Warning: transition probabilities of state %s # NULLMODEL: %g # fix_tr: %s # fix_em: # tie_em: compl_em: # #avoid states being in more than one tie group! # #avoid blank lines, especially a trailing blank line ####### ending ModelFB::WriteModelFBĝ?H_9ԝ?ModelFB::InitcumWarning cumem[last] not = 1! in ModelFB::RndEmission for state Warning cumtr[last] not = 1! in ModelFB::RndStateTransition for state ModelFB::GenerateSequence pos=%d state=%d %s letter=none pos=%d state=%d %s letter=%c pos=%d state=%d %s letter=none Failed in malloc ctiesmem Failed in malloc cties Failed in malloc tiesmem Failed in malloc ties Failed in malloc trProbmem Failed in malloc trProb Failed in malloc emProbmem Failed in malloc emProb Failed in malloc Contmem Failed in malloc Cont Failed in malloc tContmem Failed in malloc tCont Failed in malloc Contmem2 Failed in malloc Cont2 Failed in malloc tContmem2 Failed in malloc tCont2 Failed in malloc scSumEmTotmem Failed in malloc scSumTrTot Failed in malloc scEmProbmem Failed in malloc scEmProb Failed in malloc scTrProbmem Failed in malloc scTrProb Failed in malloc scForwmem Failed in malloc scForw Failed in malloc scBackwmem Failed in malloc scBackw Failed in malloc statenamesmem Failed in malloc statenames Failed in malloc PosStateProbmem Failed in malloc PosStateProb start SetUpConnections end SetUpConnections start SetUpScaledParameters emScale = %g end SetUpScaledParameters Onɞ?? start SetUpLogParameters P log viterbi-probability = %g Viterbi-path_string: %s- Viterbi-path in detail: pos seq statenb state_name %d %c %d %s log viterbi-probability = -INF Warning: Sequence %d has Probability 0; has Probability 0 Warning: Sequence Nb @ seqLen=FB computation STARTS nbStates = wFBalgo.check could not open the file FBalgo.check for writing *********************** FB computation nbStates = %d scForw[st %d][pos 0] = %6.15f; scForw[st %d][pos %d ] = %6.15f; scForw[0][pos] = %f at pos %d scFBFactor at pos %d scForw[st %d][totalNumber+1 = %d] = %6.15f; scBackw[st %d][totalNumber+1 = %d] = %6.15f; scBackw[st %d][%d ] = %6.15f; scBackw[s][0] = %6.15f; scBackw[startstate][0] = %6.15f; ; scForw[endstate][totalNumber+1=%d] = %6.15f; . Failed ForwBackw-PrecisionCheck seqNb= scBackw[startstate][0] = scForw[endstate][totalNumber+1] = Passed ForwBackw-PrecisionCheck at diff <= seqNb= pos=%d FBFactor=%d s=%d Warning: Sample with computed FB probability equal to zero Sample with computed FB probability above zerolog probability logP=%6.15f renormalised prob-score from Backw = %6.15f; ; renormalised prob-score from Forw = %6.15f; ; corrected prob from Backw = %6.15f; ; corrected log prob from Backw = %6.15f; ; corrected prob from Forw = %6.15f; ; corrected log prob from Forw = %6.15f; pos= P[pos %d][st %d] = %6.3f; PosStateProb[pos][st] st = %d pos %d = %6.15f; probSeq at pos %d = %6.15f; Failed the probSeq=1 PrecisionCheck in the method ModelFB::FBalgorithm FB computation concludedhX?-CΒ6?d start in initCodes in class ModelFB t=%d letter=%c code=%d t=%d Decode=%c finished in initCodes ModelFB::ComputeSeqBWstart ModelFB::ComputeSeqBWdsDNA1t = first state in pair = second state in pair = = Cont.A 100k+cties[t][0] = Cont.A 1 = Cont.A 2 = Cont.B 100k+cties[t][1] = finish ModelFB::ComputeSeqBWdsDNA1 ModelFB::ComputeSeqBWdsDNA2Cont2.A 100k+cties[t][0] = Cont2.B 100k+cties[t][1] = ModelFB::ComputeSeqVL end ModelFB::ComputeSeqVL start ModelFB::InitialiseBWIterStepstop ModelFB::InitialiseBWIterStep start ModelFB::Pseudocountsfinished ModelFB::Pseudocounts >YS??[eh | @AB GrAsAt&..R.E.M.N.[.E.I.L.|.m.R.E.M.N.[.E.I.L.|.m.R.E.M.N.b.L.I.L.n.m.R.E.M.N.[.E.I.L.|.m.R.E.M.N.[.E.I.L.|.m.R.E.M.N.[.E.I.L.b.W.R.E.M.N.[.E.I.L.|.m.R.E.M.N.[.E.I.L.e.6.R.L.I.L.].E.M.N.b.. 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