ELF>^@@     "%'*,.03579;=?ACEGIKMOQSUWY[]_acegikmoqsuwyz|~   !#%')+-/13579;=?ACEGIKMOQSUWY[]acefhiklnoqrtuwxz{}~HHHxw HDUHSHHT$0HL$8LD$@LL$Ht?)D$P)L$`)T$p)$)$)$)$)$HH$HT$HD$HD$HD$ D$ 0HD$HT$HHHtHHH[]f.UHSHHT$0HL$8LD$@LL$Ht?)D$P)L$`)T$p)$)$)$)$)$HH$HT$HD$HD$HD$ D$ 0HD$HT$HHHtHHH[]f.UHSHHT$0HL$8LD$@LL$Ht?)D$P)L$`)T$p)$)$)$)$)$HH$HT$HD$HD$HD$ D$ 0HD$HT$HHHtHHH[]f.UHSHHT$0HL$8LD$@LL$Ht?)D$P)L$`)T$p)$)$)$)$)$HH$HT$HD$HD$HD$ D$ 0HD$HT$HHHtHHH[]f.HYWHH@XHH9u\T. w H^HHH؃H9HGHHYv0YWHWvYWHWv YWWH9II)MIN Mt1}L11eYH})H I9wLM9t>wHYHPH9HHH9Yv*HYwfHu11ffWH@f.AWAVAUATUSHhH_o(H|$@LgLL7H\$0Ɖ9}1 9Hc)LHQHD$ H\$HZH\$8JH\$(D)\$LI\I)Ld$XH\$PHD$@H\$ WH@ H@HIFHxRHt$ T$LLl$PW HIE1HcHH|$H|$XH)IHH|$HH<$LIIHOdMIL@M9oMFOL;L${PH4$H|$I(DMt/I@H 0HIGJ1fD$ٹHL9uHHL9uXġ{IFI_HPI9^HWL$E1ġ{L\$$I\D$IF$L\$XL;`rL$(L\$ $ $HD$0L\$H|$XH@Mt$L$8tHT$(1LL$L$IF1E1HxL|$L|$(HHġ{DL$\D$L$1ġ{DMu5fDġ{DIV{,HRHT(љ{HI9uIFIH0L;hrL|$LLL$SHD$ HD$HD$8H9D$ L$_Hh[]A\A]A^A_(TWfAWHAVAUATUSHXh LxH|$HHL0H|$8Ɖ9։}1҉9H)HcЍAH<HT$WHDL,H|$(HD$@Ll$0HD$HH|$(H@H@H,8IFHxH$D$%E1E1Hl$D$In H$MDD$H|$WLXA)LL/DHIGMc{kI9LGH)M9J|vuMV0WHHHfDHHIGIV8(H48IC H 81f. \ HH9uI:HM9uXHD$IHġ{H$I_H@I9HHl$WtQIH,$d$ E1ā{DI\$\D$ L$L;eL$\$Xrd$ L(\$d$E1H$d$\$XHx|$t7IH,$ā{D$\D$ā{DIL;e$rLHD$8H|$(HH@L$8tHT$01L$$IVHzHtSLl$0111Ht6@HR{4DHT2(ə{HI9IVuHzHHHH9rHL$HD$HD$(HD$@H9D$$J\t`L1E1DMt 1HVH HHL9YuHWHFB HIHHXL;rUHH)HAUIIATISHHMH;HAff@.CHQff<.SHAf%f=.SHAf%f=.HIcLH)Ht*HtHt.HeL[A\A]];u)H;uH;tfHHe[A\A]]fHeHC[A\A]]ÐHCf.HCf.UHH)HAUIIATISHHMH;HAff@-CHQff<-SHAf%f=-SHAf%f=-HIcLH)Ht*HtHt.HeL[A\A]];u)H;uH;tfHHe[A\A]]fHeHC[A\A]]ÐHCf.HCf.UHHAWAVAUATSHH`Dh(HH|$HH|$8HxH|$0HxH|$(ADA9։}1҉9)HcHD$HAH4H|$ HHt$@Ht$8HD$HL)D$ HD>MH$HD$H|$@ WH@ H@L$8HCHx'H|$HD|$ L\$8L4$Ll$PWALl$(DHL+\$ IMc E11I)K<;H|$XfLHxM9uMMFEWM9LOI}MHD$X(L)4I HL9XuXI0{HCH_HHH9rHLl$PWL$PE1@ā{IT$X\D$PHCT$XXL;prL$P(L$XL$XHD$0H=H|$@XH@l$XL48t L1LHC1E1HxLl$PILIfġ{\D$X1H=ġ{HL$Pu4fDġ{IU{$HRJT"(ٙ{HH9uIEII0L;xrLLl$PH=t9WKT5LfXHH9u\T . w4HD$HHD$@HD$H9D$H^He[A\A]A^A_]('LH^HH؃H;HGHHH{Y{t6{YNH{Nt"{YNH{Nu{YN{NH;=L I)MIJ4Ht/}I<11Y H) H L9rHL9thwIY  HPH9IHH;Y  IY11H[HDwWLDf..|w3.+w$..w.=-Gff.UHAWIAVIAUIATSHHH`Ht$ HrHT$HL$(HLLHPC.V%HD$@HD$HHD${gH%d$KD`t$d$(XY@.E.57H|$@LHL$(Ht$HT$@H|$ HD$@WHuNHD$ PX\T ..HD$(Rxl$|$(MD$8E1HteN4E1fDII9tDHT$HJ2ġ{ . v(L$0IL$0I9L$8L$8uHD$@II9rH|*d$8^d$..D$IHt$@LH|$@HD$Hxt6 H|$1Hf.IUHHH H;GrMMH=1MLW%@Ht|IEL(H I HXHH9u=\T.v>.zt6=1^ DIUJ HHH9Y  uMMHL9rHeL[A\A]A^A_]HƒHH *XoHD$(H@Ht$H|$ HLHL$(Ht$LH|$ HD$(%`H|$@HwLHHwUHAWAVAUIATSHHGHH_ Lw(D$HL9HD$8LcHcL1H)IH9sH1HHHH9HH HD$ H$HL$0HD$(H$HD$IE@Ht$0HxHI/HD$8Ld$(LL=HDŽ$1HDŽ$`Ƅ$hƄ$iHDŽ$pL$0HDŽ$xHDŽ$HDŽ$HIGH0H$0H$0HXHH$pHDŽ$0HDŽ$HDŽ$8HDŽ$@HDŽ$HHDŽ$PHDŽ$XHDŽ$`HDŽ$hH$0LHDŽ$8DŽ$xHDŽ$Hp|$HD$PIE@LH$0L$HxIM0IU8HIvLILAHJHRH$H$8LH|$PLH$H$HxH|$PHwHXH|$8H$HT$pHHD$pHDŽ$HDŽ$HDŽ$HDŽ$HDŽ$H$L$H|$HDŽ$HDŽ$LHH$LHHx$H|$8H$H$HH$Ht$pH$HDŽ$HDŽ$LHD$8Hxx_1H$ID$t7Ld$IH@H$HB4 IL;$rLd$It$H$H$IUMNIuI}LAH$Ht$OHxH$Ht$OHDŽ$HDŽ$HDŽ$HDŽ$HxI|$PHDŽ$HHI|$hH$H@HHHH$H@HHHH$H@HHDŽ$HDŽ$H$HtH$Ht$OHxH$HtH$Ht"H8HtH$HtHH$Ht$OHxH$HtH$H$Ht$OHxHD$pHt$OHxHD$PHt$OHxH$Ht$OHDŽ$0HDŽ$HDŽ$8HxH$pHDŽ$8L$0HIGH0H|$(HDŽ$HD$0HD$0H9D$ He[A\A]A^A_]IE@LHxHL$HD$PLHxH$8HDŽ$0HDŽ$NH$LHx(IV14HHt$pH$H$HDŽ$H51DH$HH v=1Ҹ ._HGHH9uH$8HH9u1wH$HDŽ$H$wH$LHxwHHwHHL$RH\$8IVH1H{(H$HD$pLHxMH$8wL$0HIGH0w-fUHAWAVAUATSHH0H_Do H<$L'H\$H_H\$D9}1؉\$,9ÉD$(+ID$ L-LcHD$JN<IH$L$,I|$HT$Ht$H@H@J0IHD$MH@J 0tHL1HL$ HL$ IT$LBMtM11@1Mt1HRHT:(HI9IT$uLBHHHL9rMt9WIHXHH9u%\T . w&D$,ID$(9D$,He[A\A]A^A_]H^LHH؃L9IGIHHY  t0YIHItYIHIu YIIL9cMI)MIJ<Ht1}L11mY H}) H L9rHL9t`wHY  HPL9HHL9Y  HY11HeHDwq]ZHGG-@HHHGGGHW XXY_^]GGHHHHHHHHUsage: cstranslate -i [options] Translate a sequence/alignment into an abstract state alphabet. Input file with alignment or sequenceOutput file for generated abstract state sequence (def: .as)Append generated abstract state sequence to this fileInput format: prf, seq, fas, a2m, a3m or ca3m-I, --informat prf|seq|fas|...Outformat: abstract state sequence or profileMake all FASTA columns with less than X% gaps match columns(def: make columns with residue in first sequence match columns)Abstract state alphabet consisting of exactly 219 statesAdd context-specific pseudocounts using given context-dataPseudocount admix for context-specific pseudocountsConstant in pseudocount calculation for alignmentsWeight of abstract state column in emission calculationRead from -i , write to -o (do not include _ca3m suffix for ca3m informat); enables openmp if possibleBackground frequencies on query side (in %): Background frequencies on database side (in %): Substitution matrix log( q(a,b) / p(a)*p(b) ) (scaled by 1/lambda): Target frequency matrix q(a,b) (in %): Matrix of conditional probs on query side P(a|b) = P(a,b)/p(b) (in %): Matrix of conditional probs on database side P(a|b) = P(a,b)/p(b) (in %): %s abstract state sequence to %s %s abstract state count profile to %s Stream does not start with class id 'CountProfile'!Unable to parse count profile 'NAME'!Unable to parse count profile 'LENG'!Unable to parse count profile 'ALPH'!Alphabet size of serialized count profile should be %d but is actually %d!Count profile should have %i columns but actually has %i!Invalid character with ASCII number %i at position %zu of sequence '%s'Sequence header does not start with '>'!Stream does not start with class id 'ContextProfile'!Unable to parse context profile 'NAME'!Unable to parse context profile 'PRIOR'!Unable to parse context profile 'COLOR'!Unable to parse context profile 'ISLOG'!Unable to parse context profile 'LENG'!Unable to parse context profile 'ALPH'!Alphabet size of serialized context profile should be %dbut is actually %d!Context profile should have %i columns but actually has %i!Stream does not start with class id 'ContextLibrary'!Unable to parse context library 'SIZE'!Unable to parse context library 'LENG'!Serialized context library should have %i profiles butactually has %i!Reading abstract state alphabet from %s ... Abstract state alphabet should have %zu states but actually has %zu states! Abstract state alphabet should have a window length of %d but actually has %zu! Stream does not start with class id 'CrfState'!Unable to parse CRF state 'NAME'!Unable to parse CRF state 'BIAS'!Unable to parse CRF state 'LENG'!Unable to parse CRF state 'ALPH'!Alphabet size of serialized CRF state should be %dbut is actually %d!CRF state should have %i columns but actually has %i!Stream does not start with class id 'CRF'!Serialized CRF should have %i states but actually has %i!Reading context library for pseudocounts from %s ... Reading CRF for pseudocounts from %s ... Header of sequence %i starts with: %sBad alignment: no alignment data found in stream!Sequence %i has %i match columns but should have %i!Sequence %i in A3M alignment contains gaps!Error: different number of sequences in blocks 1 and %i.Error: Missing whitespace between identifier and sequence characters of sequence %i in block %i.Error: Missing sequence characters in sequence %i of block %i.Bad alignment dimensions: nseqs=%i ncols=%iBad alignment: unequal number of headers and sequences!Alignment sequence %i has length %i but should have %i!Invalid character %c at position %i of sequence '%s'Unsupported alignment input format %i!Adding cs-pseudocounts (admix=%.2f) ... Unknown alignment format extension '%s'!Could not read entry: %s, Message: %s Unable to read input file '%s'!Translating count profile to abstract state alphabet AS219 ... HO()HO(@-i, --infile %-30s %s -o, --outfile -a, --append %-30s %s (def=%s) -O, --outformat seq|prf-M, --match-assign [0:100]-A, --alphabet %-30s %s (def=internal) -D, --context-data -x, --pc-admix [0,1] %-30s %s (def=%-.2f) -c, --pc-ali [0,inf[ %-30s %s (def=%-.1f) -w, --weight [0,inf[-f, --ffindex %-30s %s (def=off) %d%+5.1f %-.2f %-.1f basic_string::substrinfileoutfileappendfileinformatoutformatmatch-assignpc-admixpc-alialphabetcontext-dataweightffindexverboseNo input file provided!No abstract states provided!stdoutauto.asseqinternalcstranslateawappendwriteAppendedWroteCan't %s to file '%s'!CountProfile NAME %s LENG %zu ALPH %zu COUNTS NEFF %c// %zu * %d %d Can't %s to output file '%s'!CountProfileNAMELENGALPHContextProfilePRIORCOLORISLOGContextLibrarySIZErUnable to read file ''! CrfStateBIASCRFUnable to parse CRF 'SIZE'!Unable to parse CRF 'LENG'!libcrfInvalid pseudocount engine: >ss_>sa_ss_predss_confss_dsspvector::_M_default_appendprffasmfaa3mca3mpsia2mcluProcessing entry: %s stdinPosConsAS219Conf.ffdata.ffindex_ca3m.ffdata_ca3m.ffindex_header.ffdata_header.ffindex_sequence.ffdata_sequence.ffindexSHH(1H{(1H{(1H{(LCp1LCxH{(1H{(1H{(1H{(1H{(1H{(H{(H{(H{([1UHSHHhfft-H[]UHSHHhfft.H[]HHVH)HHtHu"HHHH1f.1H9tHSHHH8HtH{0HtH[SHHH8HtH{0HtHH[USHHHHHt/H}HtH}HtHHǃHHtHPHǃHHtHPHǃHHtHPHǃHHtHPHǃHCxHt$HC@HxHCpHt$HxHChHt$HxHC`Ht$HxHCXHt$HxHCPHt$HxHCHHt$HxHH[]SHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHu HH[ùHWHtHt$΋PJHSHHHGHHxHuHH[ùHWHtHt$͋PJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHHxHuH{8HH[ùHWHtHt$ŋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHGHHxHuHHH[ùHWHtHt$ƋPJHSHHHG HHxHu%HCHHxHu2HH[ùHWHt<Ht$붹HWHt$Ht$멋PJH뾋PJHSHHHGHHxHuHHH[ùHWHtHt$ŋPJHSHHHGHHHxHuH{8HHH[ùHWHtHt$뽋PJHSHHHG HHxHu-HCHHxHu:HHH[ùHWHt<Ht$뮹HWHt$Ht$롋PJH뾋PJHUSHHHHHt/H}HtH}HtHHǃHHtHPHǃHHtHPHǃHHtHPHǃHHtHPHǃHCxHt$HC@HxHCpHt$HxHChHt$HxHC`Ht$HxHCXHt$HxHCPHt$HxHCHHt$HxHHH[]U-HAWAVIAUATSHHHHL%ME1DAHt$HID$HM9uHE1@IFp%H$ġ[YH$HHVH$H$IHxM9u1HE1@AHt$0HID$0HM9uHE1@I-H$ġSYH$HHVH$H$IHxM9uEHE1fAHt$PHID$PHM9uHHD$fDHD$E1L<IF0H$J8ġ{H$HHVH$H$IHxM9uHH@LMA}8AECHHHD$L9d$I'HE1@AHt$pHID$pHM9uHHD$fDHD$E1L<IF H$J8ġsYH$HHVH$H$IHxM9rHH@LMA}8AECHHHD$L9d$AGHE1@AH$HI$HM9rHHD$HD$E1L<IFHH$J8ġkYH$HHVH$H$IHxM9rHH@LMA}8AECHHHD$L9d$AJHE1@AH$HI$HM9rHHD$HD$E1L<IF`H$J8ġcYH$HHVH$H$IHxM9rHH@LMA}8AECHHHD$L9d$AHe[A\A]A^A_]fLIE LP0'@LIE LP0/@LIE LP0?@LIE LP0OH1HHEHH'HHGHHHߺJHHe[A\A]A^A_]HH$H$HxwHfL+}    SHHHG8HHxHu|HC0HxHHC(HxH HC HxH&HCHxHHCHxHupHCHxHu6H[ùHWH3cHt$THWHHt$롹HWHoHt$`HWH.Ht$HWHHt$HWHHt$HWHt>cHt$TPJHPJHPJH뼋PJHPJH@PJHPJHPSHHHG8HHxHHC0HxHHC(HxHHC HxH.HCHxHHCHxHuxHCHxHu>HH[ùHWH3[Ht$LHWHHt$뙹HWHgHt$XHWH&Ht$HWHHt$HWHHt$HWHt>[Ht$LPJHPJHPJH뼋PJHPJH@PJHPJHPUSHHHHGCH[]HHwH(9AUATUHSHHT$0HL$8LD$@LL$Ht?)D$P)L$`)T$p)$)$)$)$)$ILd$HEHEEHH$Ld$LHD$HD$HD$ LD$ 0HD$HH}HHHtHH[]A\A]HHELHxwHH YATIUHSHHHHJЀ HtHJHzHq@ wtFH9s:-tF 1H QЀ wDH3VЀ v[]A\@Mu#[]A\ú 1비tH롿LHH1HHHwH ATIUHSHHtHH<1[]A\fMu []A\ÿLHH1HHHwHWniAUIATIUHSHHHHHHtkHHtVH+@tMHHH+@t3Dj uHHHLHL[]A\A]1@MtݿLHH1HHwI<$Ht$HHHHwHuUHAVIAUATISHHILLHLHpҁ t€DHHHDHL)HcЀ<zIT Hzfu$H$mHLHHPDZ uH@LLL9He[A\A]A^]fHc=~L u|AUAATUHSHHHH/HPHI|EHuGHP.HL9v.Ht(LIT$HHHH;Pv(HH@IT$HL)H9wHHHH[]A\A]Eu+H.HHPHtH1f.HHHH[]A\A]UHGHHAWIAVAUIATSHHHĀH|$ HT$H$H|$PHt$ HD$@D$HiHL$@LL|$XHD$@Hy Ht$@LHD$`Ld$HD$@L{PLHxHD$PLHD$@HxHD$ Ht$@HxH|$ HT$H|$PHt$ HD$@D$HoH|$`LL|$XHD$@Ht$@LHD$`LHD$@LsXHxHD$PLHD$@HxHD$ Ht$@HxH|$ HT$H|$PHt$ HD$@D$HaH|$`LLt$XHD$@Ht$@LHD$`LHD$@LspHxHD$PLHD$@HxHD$ Ht$@HxH|$ HT$H|$PHt$ HD$@D$HIH|$`LLt$XHD$@Ht$@LHD$`LHD$@HxHD$PLHD$@HxHD$ Ht$@HxHCxH|$ HT$HD$HL$@Ht$ HD$@D$HOHyHD$HL$@HD$@Hy HHD$XHt$@LHD$`LHD$@HxHD$PLHD$@HxHD$ Ht$@HxHH|$ HT$HD$HL$@Ht$ HD$@D$HMHyHD$Ht$@LHD$@HD$XD$`HD$PLHD$@HxHD$ Ht$@HxHH|$ HT$HD$HL$@Ht$ HD$@D$HxHyHD$Ht$@LHD$@D$`HD$XHD$PLHD$@HxHD$ Ht$@HxHH|$ HT$HD$HL$@Ht$ HD$@D$HcHyHD$Ht$@LHD$@D$`HD$XHD$PLHD$@HxHD$ Ht$@HxHChH|$ HT$HD$HL$@Ht$ HD$@D$HAHyHD$HL$@HD$@Hy HHD$XHt$@LHD$`LHD$@HxHD$PLHD$@HxHD$ Ht$@HxHC`H|$ HT$HD$HL$@Ht$ HD$@D$HDHyHD$HL$@HD$@Hy HHD$XHt$@LHD$`LHD$@HxHD$PLHD$@HxHD$ Ht$@HxHH|$ HT$HD$HL$@Ht$ HD$@D$HwHyHD$Ht$@LHD$@D$`HD$XHD$PLHD$@HxHD$ Ht$@HxHH|$ HT$HD$HL$@Ht$ HD$@D$HfHyHD$Ht$@LHD$XHD$PLHD$@HxHD$ Ht$@HxHH|$ HT$HD$HL$@Ht$ HD$@D$HvHyHD$Ht$@LHD$@HD$XD$`HD$PLHD$@HxHD$ Ht$@HxHCHHxXHChHxwLuƃHCPHxuoHCXHxudH4$H|$ 1H|$ HHt$@LHT$@HHD$@LHxHD$ Ht$@HxLtHe[A\A]A^A_]fHCHH<$.HPHt\HSHHrHPHH)H9H4$H|$@Ht$@LHD$@Ht$ HxHe[A\A]A^A_]@HT$ H|$@뷿HH1HHH1пH|$@HwHD$ LHxHHHD$@HD$PLHxwHD$@HHD$@wHHD$@HD$PLHxwHHD$@^f.xf.=fXf.sf.afSf.f.f.#f.f.f.Ld$HHD$@wH|$@HwLd$|HHD$@Ld$HHD$@HwHD$ Ht$@HxHHHD$@Ht$ HxwHHHD$@LHxw4h#HHD$@3IHwL5Rq~             6fUSHH0HHGHGHGHGHGHGHHGH{8H{ H{(CP CqCp%C@KHSX[`chH[]HHC8Ht$HxwHC0Ht$HxHC(Ht$HxHC Ht$HxHCHt$HxHCHt$HxH{Ht$HH V>UHAUATISHH H|$ HT$H|$@1L-HH|$@HD$@HD$@Hx@LD$ H|$@LLHDŽ$HDŽ$HDŽ$HDŽ$HDŽ$H|$@D$ HD$ Ht$@HxD$ He[A\A]]HwHD$ Ht$HxHH|$@HwH|$@Hw@HH(H_"^  "" "1K3_y0_~0(L|     (  4E3     F  #16")S]  N3OJAx}(X5B2*&2$N"+(L|   &   3*dLn0    i    p     v>c       <  .VoA7z}y! 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