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Pritchard Jan 2000 (minor changes 5/2000) Version %s free error 1 free error 2 free error 3 free error 4 free error 5 free error 6 free error 7 free error 8 free error 9 free error 10 free error 11 free error 12 free error 13 free error 14 free error 15 Translation matrix: %2d %d Starting from a random configuration because POP=0 USING GIVEN POPULATION INFO TO SET INITIAL CONDITION WARNING: unable to initialize %d individuals to the predefined populations because their population names were not in the range {1..%d}. These individuals were initialized at random. Error in assigning memory, InitFreqPriors WARNING: expected allele value, InitFreqPriors: loc %d, allele %d MIGRPRIOR (which is currently set to %1.3f) must be in the range [0.0, 1.0] Can't apply USEPOPINFO because no POPDATA in input data file Warning: population prior for individual %d is %d, which is not in the range 1..%d. Population prior for this individual will be ignored *0.++??WARNING: unable to allocate array space in UpdateP WARNING: error in assigning memory in function UpdateQMetro Acceptance rate in UpdateQMetro %1.3f Error in CalcLikeInd 0.++Warning!! Error in assigning memory in UpdateQWithPops 0.++??WARNING: unable to allocate array space in UpdateZ Error in assigning memory (not enough space?) -------------------------------------- Finished initialization; starting MCMC %d iterations + %d burnin ?0.++?mainparamsextraparamsSTRATparamsdefineReading value of "%s" INFILEOUTFILENUMINDS%dNUMLOCIMISSINGLABELPOPDATAPOPFLAGPHENOTYPEEXTRACOLSMAXPOPSBURNINNUMREPSUSEPOPINFOINFERALPHACOMPUTEPROBNOADMIXNOADMBURNPRINTQHATUPDATEFREQPICTUREFILEPRINTLIKESINTERMEDSAVEPRINTKLDECHODATAANCESTDISTNUMBOXESANCESTPINT%lfGENSBACKMIGRPRIORALPHAFREQSCORRCORRACORRBEPSILONUNIFPRIORALPHAALPHAMAXALPHAPRIORAALPHAPRIORBALPHAPROPSDFPROPSDSTARTATPOPINFORANDOMIZEMETROFREQREPORTHITRATENUMSIMSTATSEMERRORNUMPHENSPOOLFREQLOCUSxONLYWarning: Ignoring unrecognized parameter name (%s) rCan't open the file "%s". Reading file "%s". outputNeed to specify the name of the data file Need to set NUMINDS>0 in the file mainparams Need to set NUMLOCI>0 in the file mainparams Need to set LABEL=0 or 1 in the file mainparams Need to set POPDATA=0 or 1 in the file mainparams Need to set POPFLAG=0 or 1 in the file mainparams Need to set PHENOTYPE=0 or 1 in the file mainparams Need to set EXTRACOLS>=0 in the file mainparams Need to set MAXPOPS>0 in the file mainparams Need to set PHENOTYPE=1 in the file mainparams to run STRAT Need to set EMERROR>0 in the file STRATparams Need to set NUMPHENS>1 in the file STRATparams Values of parameters used in structure: DATAFILE=%s, OUTFILE=%s, NUMINDS=%d, NUMLOCI=%d, MISSING=%d, LABEL=%d, POPDATA=%d, POPFLAG=%d, PHENOTYPE=%d, EXTRACOLS=%d, MAXPOPS=%d, BURNIN=%d, NUMREPS=%d, USEPOPINFO=%d, INFERALPHA=%d, COMPUTEPROB=%d, NOADMIX=%d, NOADMBURN=%d, UPDATEFREQ=%d, PRINTLIKES=%d, INTERMEDSAVE=%d, PRINTKLD=%d, ANCESTDIST=%d, NUMBOXES=%d, ANCESTPINT=%1.5f, GENSBACK=%d, MIGRPRIOR=%1.5f, PRINTQHAT=%d, ALPHA=%1.4f, FREQSCORR=%d, CORRA=%1.4f, CORRB=%1.4f, EPSILON=%1.4f, UNIFPRIORALPHA=%d, ALPHAMAX=%1.4f, ALPHAPRIORA=%1.4f, ALPHAPRIORB=%1.4f, ALPHAPROPSD=%1.4f, FPROPSD=%1.4f, STARTATPOPINFO=%d, RANDOMIZE=%d, METROFREQ=%d, REPORTHITRATE=%d, Reading file "%s". rUnable to open the file %s. labelpoppopflagphenotype WARNING: Unexpected end of input file. The details of the input file are set in mainparams. I ran out of data while reading the data for individual %d. WARNING! Possible error in the input file. Non-integer value in an unexpected place: encountered %s while reading the data for individual %d WARNING! Possible error in the input file. Non-Real number in an unexpected place: encountered %s while reading WARNING! Possible error in the input file. The value of %s does not agree across lines for individual %d WARNING: There may be more data in the input file than indicated by the program constants. Check the values entered for NUMLOCI and NUMINDS, etc, in the program constants. Data file "%s" (truncated) -- Ind: Label%5s Pop Flag Phen : Genotype_data . . . . %3d: %4d :%3d . . . . %3d ******* ---------------------------------- There were errors in the input file (listed above). According to "mainparams" the input file should contain %d rows with %d entries in each row. Warning: error assigning memory in CountLineLens There are %d rows of data in the input file, with an average of %1.2f entries per line. The following shows the number of entries in each line of the input file: # Entries: Line numbers %4d: %d, , %d--%dNumber of alleles per locus: min=%2d; ave=%2.1f; max=%2d maxk = %d, MAXALLELES = %d Program error in function CountAlleles Aborting the program due to error(s) listed above. %6.0f BURNIN completed Admixture Burnin complete. Current alpha = %1.3f %5d: %1.3f %2.1f %.0f %.0f $@ Rep#: Alpha Corr D%d,%d Ln Like Est Ln P(D)%1.3f Allele-freq. divergence among pops (Kullback-Leibler distance), computed using point estimates of P. %2d %2d - %2.2f ?Input File: %s Output File: %s_f Run parameters: %d individuals %d loci %d populations assumed %d Burn-in period %d Reps USEPOPINFO turned on MIGRPRIOR = %1.4f NO ADMIXTURE model assumed STARTATPOPINFO turned on RANDOMIZE turned off (%1.3f,%1.3f) %1.3f | Pop %d: | *?333333??Inferred ancestry of individuals: Probability of being from assumed population | prob of other pops Label %8s (%Miss) Pop: Inferred clusters (and %d%c probability intervals)%3d %8s (%d) %2d : Y@?%s_qwWARNING: Unable to open output file %s. %12s %4d %1.4f Estimated Allele Frequencies in each population Locus %d %d alleles Average correlation factor = %2.1f %2.1f%c missing data %4d -------------------------------------------- Estimated Ln Prob of Data = %1.1f Mean value of ln likelihood = %1.1f Variance of ln likelihood = %1.1f Mean value of alpha = %1.4f Mean value of allele freq corr = %1.4f Allele frequencies uncorrelated Error assigning memory in function PrintMembership -------------------------------------------- Proportion of membership of each pre-defined population in each of the %d clusters Given Inferred Clusters Pop %2d %3d: %1.3f Overall proportion of membership of the sample in each of the %d clusters Inferred Clusters %2d %s_f%s_%d MCMC completed Final results printed to file %s ?Y@0.++??Y@?ݰ @>@@@(\???$@@V_?>lHE?.iqUU?333333?-@6$I?.@F@@ Ac]??M OiKGUU?333333@??Zd;O???>?@@?>?>?@@?>>>?>>>?Division by zero in variance calculation. WARNING: trying to compute %d! Warning error assigning memory in ChiSq ????N~h?t\࿇1UU?hqп14?0>qCſq53?ϸg"T2???@@8@^@@@@&A r?i?-s,&?"?I:?Yqo\?0q?Z䍂d?#^ ?4w?v|?CH?@8?a@@?! ?k?d8/?܇r?O?5>8Dc?VnX L?4F(?j=?_Zg?k{?J̳?5K?1v‹? v?g?B`";@h=4?B@ ?d?(W?}?AN?)c2?8? L[?+{?x?g@?`?%?ʗ4Ǩ?Vc5?z*@?6nf?B% ?mc?! ? Q$?0?ӊ?2/)ㄼ?Hr?9F%I?Zfb?׬Mo?!Fv?(]1|?\9* Ձ?$X?rpe`O?fa֌?p?xkO?POE?]t[?Ǭjc ?Q~s?ӆ??.?!1? 륭:@?P0Qc?Ait?Ґȩ?T ?$?Ŵ?3N9?Wh?6x?J ]?X"?-Y&?ՋF? ?A2Ӭ"? ܺ:?E[?K-??}5?:S9?Sꋥ???mbqW??MNiԦ?,fb?Ȼ<V?,Y?8j?}qq?tl-a?mwͳ?'>-z?LkT&?jn}??\=䘲?J-)J?7R{?sovRk?h˹W?yߝ!?d ?)?>Dn? j C.?I2?W?0v?p"?zA?wa?? \\JZjzʆچ *:JZjz!  "(  x\\Looo(dćdć$<3b|%q 3Xr .Xl !bv! M1h(;!g$B?!  %!="S#j%&12345 60 8I 9c ; = > ? @ A B C0 DI E` Fy G H I N Q R9 SQ Tj V Y o r u {6 |S o  8 R F   +"jG3;BE0nRY ])fkPshx! #$%& "dćinit.c/usr/src/bs/BUILD/glibc/csu/gcc2_compiled.int:t(0,1)=r(0,1);0020000000000;0017777777777;char:t(0,2)=r(0,2);0;127;long int:t(0,3)=r(0,1);0020000000000;0017777777777;unsigned int:t(0,4)=r(0,1);0000000000000;0037777777777;long unsigned int:t(0,5)=r(0,1);0000000000000;0037777777777;long long int:t(0,6)=r(0,1);01000000000000000000000;0777777777777777777777;long long unsigned int:t(0,7)=r(0,1);0000000000000;01777777777777777777777;short int:t(0,8)=r(0,8);-32768;32767;short unsigned int:t(0,9)=r(0,9);0;65535;signed char:t(0,10)=r(0,10);-128;127;unsigned char:t(0,11)=r(0,11);0;255;float:t(0,12)=r(0,1);4;0;double:t(0,13)=r(0,1);8;0;long double:t(0,14)=r(0,1);12;0;complex int:t(0,15)=s8real:(0,1),0,32;imag:(0,1),32,32;;complex float:t(0,16)=r(0,16);4;0;complex double:t(0,17)=r(0,17);8;0;complex long double:t(0,18)=r(0,18);12;0;void:t(0,19)=(0,19)../include/libc-symbols.h/usr/src/bs/BUILD/glibc/build-i386-linux/config.h../include/libintl.h../intl/libintl.h../include/features.h../include/sys/cdefs.h../misc/sys/cdefs.h/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66/include/stddef.h../include/locale.h../locale/locale.hlconv:T(10,1)=s48decimal_point:(10,2)=*(0,2),0,32;thousands_sep:(10,2),32,32;\grouping:(10,2),64,32;int_curr_symbol:(10,2),96,32;\currency_symbol:(10,2),128,32;mon_decimal_point:(10,2),160,32;\mon_thousands_sep:(10,2),192,32;mon_grouping:(10,2),224,32;\positive_sign:(10,2),256,32;negative_sign:(10,2),288,32;\int_frac_digits:(0,2),320,8;frac_digits:(0,2),328,8;\p_cs_precedes:(0,2),336,8;p_sep_by_space:(0,2),344,8;\n_cs_precedes:(0,2),352,8;n_sep_by_space:(0,2),360,8;\p_sign_posn:(0,2),368,8;n_sign_posn:(0,2),376,8;;../include/xlocale.h../locale/xlocale.h__locale_struct:T(13,1)=s36__locales:(13,2)=ar(0,1);0;5;(13,3)=*(13,4)=xslocale_data:,0,192;\__ctype_b:(13,5)=*(0,9),192,32;__ctype_tolower:(13,6)=*(0,1),224,32;\__ctype_toupper:(13,6),256,32;;__locale_t:t(13,7)=(13,8)=*(13,1)../sysdeps/unix/sysv/linux/_G_config.h../sysdeps/unix/sysv/linux/bits/types.hsize_t:t(16,1)=(0,4)__u_char:t(15,1)=(0,11)__u_short:t(15,2)=(0,9)__u_int:t(15,3)=(0,4)__u_long:t(15,4)=(0,5)__u_quad_t:t(15,5)=(0,7)__quad_t:t(15,6)=(0,6)__int8_t:t(15,7)=(0,10)__uint8_t:t(15,8)=(0,11)__int16_t:t(15,9)=(0,8)__uint16_t:t(15,10)=(0,9)__int32_t:t(15,11)=(0,1)__uint32_t:t(15,12)=(0,4)__int64_t:t(15,13)=(0,6)__uint64_t:t(15,14)=(0,7)__qaddr_t:t(15,15)=(15,16)=*(15,6)__dev_t:t(15,17)=(15,5)__uid_t:t(15,18)=(15,3)__gid_t:t(15,19)=(15,3)__ino_t:t(15,20)=(15,4)__mode_t:t(15,21)=(15,3)__nlink_t:t(15,22)=(15,3)__off_t:t(15,23)=(0,3)__loff_t:t(15,24)=(15,6)__pid_t:t(15,25)=(0,1)__ssize_t:t(15,26)=(0,1)__rlim_t:t(15,27)=(0,3)__rlim64_t:t(15,28)=(15,6)__id_t:t(15,29)=(15,3)__fsid_t:t(15,30)=(15,31)=s8__val:(15,32)=ar(0,1);0;1;(0,1),0,64;;__daddr_t:t(15,33)=(0,1)__caddr_t:t(15,34)=(10,2)__time_t:t(15,35)=(0,3)__swblk_t:t(15,36)=(0,3)__clock_t:t(15,37)=(0,3)__fd_mask:t(15,38)=(0,5)__fd_set:t(15,39)=(15,40)=s128fds_bits:(15,41)=ar(0,1);0;31;(15,38),0,1024;;__key_t:t(15,42)=(0,1)__ipc_pid_t:t(15,43)=(0,9)__blkcnt_t:t(15,44)=(15,4)__blkcnt64_t:t(15,45)=(15,5)__fsblkcnt_t:t(15,46)=(0,3)__fsblkcnt64_t:t(15,47)=(15,6)__fsfilcnt_t:t(15,48)=(15,4)__fsfilcnt64_t:t(15,49)=(15,5)__ino64_t:t(15,50)=(15,4)__off64_t:t(15,51)=(15,24)__t_scalar_t:t(15,52)=(0,1)__t_uscalar_t:t(15,53)=(0,4)__intptr_t:t(15,54)=(0,1)../linuxthreads/sysdeps/pthread/bits/pthreadtypes.h../sysdeps/unix/sysv/linux/bits/sched.h__sched_param:T(18,1)=s4sched_priority:(0,1),0,32;;_pthread_fastlock:T(17,1)=s8__status:(0,3),0,32;__spinlock:(0,1),32,32;;_pthread_descr:t(17,2)=(17,3)=*(17,4)=xs_pthread_descr_struct:pthread_attr_t:t(17,5)=(17,6)=s36__detachstate:(0,1),0,32;\__schedpolicy:(0,1),32,32;__schedparam:(18,1),64,32;\__inheritsched:(0,1),96,32;__scope:(0,1),128,32;\__guardsize:(16,1),160,32;__stackaddr_set:(0,1),192,32;\__stackaddr:(17,7)=*(0,19),224,32;__stacksize:(16,1),256,32;;pthread_cond_t:t(17,8)=(17,9)=s12__c_lock:(17,1),0,64;\__c_waiting:(17,2),64,32;;pthread_condattr_t:t(17,10)=(17,11)=s4__dummy:(0,1),0,32;;pthread_key_t:t(17,12)=(0,4)pthread_mutex_t:t(17,13)=(17,14)=s24__m_reserved:(0,1),0,32;\__m_count:(0,1),32,32;__m_owner:(17,2),64,32;\__m_kind:(0,1),96,32;__m_lock:(17,1),128,64;;pthread_mutexattr_t:t(17,15)=(17,16)=s4__mutexkind:(0,1),0,32;;pthread_once_t:t(17,17)=(0,1)pthread_rwlock_t:t(17,18)=(17,19)=s32__rw_lock:(17,1),0,64;\__rw_readers:(0,1),64,32;__rw_writer:(17,2),96,32;\__rw_read_waiting:(17,2),128,32;__rw_write_waiting:(17,2),160,32;\__rw_kind:(0,1),192,32;__rw_pshared:(0,1),224,32;;pthread_rwlockattr_t:t(17,20)=(17,21)=s8__lockkind:(0,1),0,32;\__pshared:(0,1),32,32;;pthread_t:t(17,22)=(0,5)wchar_t:t(19,1)=(0,3)wint_t:t(19,2)=(0,4)_G_int16_t:t(14,1)=(0,8)_G_int32_t:t(14,2)=(0,1)_G_uint16_t:t(14,3)=(0,9)_G_uint32_t:t(14,4)=(0,4)_IO_stdin_used:G(0,1)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)GCC: (GNU) egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)01.0101.0101.0101.0101.0101.0101.0101.0101.0101.0101.01.symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.got.rel.bss.rel.plt.init.plt.text.fini.rodata.data.eh_frame.ctors.dtors.got.dynamic.bss.stab.stabstr.comment.note# 1((7 ?%Go6To`c LLl TTu \\ ~/44`\" # #  W D d\dh\hp\px\xd\]  D ( $  (LT \  4  " # Wd\h\p\x\\] ć " Ї -$W1p\?(WKЇ ad\t ]  @ ,Wh\" " " l\" d\t\d\ "  P        @ &@W0HW7PW>XWE`WLhWSpWZxWaWhWoWvW}WWWWWP]]]]]]]]]]]^^^ ^ ^(^%0^,8^3@^:H^@P^JX^P`^Wh^^p^ex^k^q^w^}^^^^ X Y Z [_____```` ` \@(`0`8`@`H`&P`/`\6  ? J``R"i ^d`k8J xa~ D"h`p`x`8 # " z a|`E J Ե& , ̉/ #\,$ =D C6 O V"]Tt"~d: `x8 `` t$p `[ b `#- 2p 9,  D S`[8x i`x| `  Z , P: @ 8  - `` \ <Q `$(hn 3 =`G`R"u(4 ~`9  ]`8 % (_ | ``8n  h 0X >D6 M`- XAhT] y i ,1 `a `' a aa < y ĆRa% +"= 5 CԆ"U `P| paxa a]   $aW ԏz s (a0a T8  8a   " W - )? ; O  Z @ac "i | ] x Da   Ha m  T T"  8 La Pa L `a a $" a( @ 7 ]> aI x\_ 4"o at 4J x a a P^  J a \6 a ; a a Dy  a ػ{ $# a \ ' u 0 T$C  N 4 ] Wj P z L d  @ "initfini.cgcc2_compiled.init.ccrtstuff.cp.2__DTOR_LIST__completed.3__do_global_dtors_aux__EH_FRAME_BEGIN__fini_dummyobject.8frame_dummyinit_dummyforce_to_data__CTOR_LIST____do_global_ctors_aux__CTOR_END____DTOR_END____FRAME_END__structure.cparams.cdatain.coutput.cran.cnprev.260c1.261c2.262c3.263c4.264c5.265a0.270a1.271a2.272a3.273a4.274a5.275a6.276a7.277muold.278muprev.279fact.280ignpoi.281j.282k.283kflag.284l.285m.286b1.287b2.288c.289c0.290c1.291c2.292c3.293d.294del.295difmuk.296e.297fk.298fx.299fy.300g.301omega.302p.303p0.304px.305py.306q.307s.308t.309u.310v.311x.312xx.313pp.314a.319d.320t.321h.322i.323snorm.324u.325s.326ustar.327aa.328w.329y.330tt.331RExpon.334q.337i.338sexpo.339a.340u.341ustar.342umin.343q1.344mymath.cPrintQFilePOPFLAGRandomOrderINTERMEDSAVEPickAnOptionINPUTUpdateQfgetc@@GLIBC_2.0NUMSIMSTATSALPHAPRIORAMISSINGsnormExtraDataCalcLikeIndBinomialPARAMSLABELfsignRandomIntegerInitializationRandomRealInitializeZ_DYNAMICPrintTranslationKLDivPrintUpdateRExpon_etext__register_frame_info@@GLIBC_2.0strcmp@@GLIBC_2.0KillNUMBOXES_fp_hwPrintLikeCOMPUTEPROBREPORTHITRATEInitFreqPriorsfprintf@@GLIBC_2.0ChiSqUSEPOPINFOMissingIndCheckIfValidDoubleALPHAMAXAlphaPriorDiffignpoiPrintGeogQLDirichletProbFPROPSDGetNumLociPopSTARTATPOPINFODataCollectionUPDATEFREQReadDataUpdateSumsgenunfUpdateFreqPriorsRGammaRPoissonReadFileMAXALLELESBURNIN_initCheckIfValidIntReadInputFileDATAFILEfscanf@@GLIBC_2.0MissingLocRandomizeNOADMBURNLOCUSxONLY__deregister_frame_info@@GLIBC_2.0OpenDataMETROFREQSampleVarUpdateQWithPopsstdout@@GLIBC_2.0EMERRORPrintBannerabort@@GLIBC_2.0MismatchPrintAllParamsCountAllelesEPSILONPOOLFREQBinoProbUpdatePPrintAncestDistSetUpdateFreqFindMaxAllelesFPriorDifftime@@GLIBC_2.0UpdateQAdmixture_startRDirichletUpdateAlphaGENSBACKWelcomeALPHAPROPSDAveFMAXPOPSPrintSomeDataANCESTPINTECHODATAFindAveLogsGetParams__strtol_internal@@GLIBC_2.0UNIFPRIORALPHAsexpoFactorialGetNumFromPoplgamma@@GLIBC_2.0ReadStringInitFromGeogPopNUMREPSINFERALPHAFREQSCORR__bss_startCalcLikemainEXTRACOLSGetParamValue__libc_start_main@@GLIBC_2.0LogProbQUpdateQMetroCORRAORIGMISSINGPresetValuesMIGRPRIORSquaredata_startprintf@@GLIBC_2.0PrintMainParamsWhitespacePRINTKLD_finiLGammaDistProbNOADMIXFreeAllfclose@@GLIBC_2.1NUMINDSSDPrintSumsCountLineLenssrand@@GLIBC_2.0CheckIfMissingPrintPPRINTLIKESPRINTQHATPrintQOUTFILEALPHAcalloc@@GLIBC_2.0POPDATAUpdateQNoAdmix_edataANCESTDIST_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endrndPHENOTYPENOALPHAUpdateZBinomial1ignuinNUMLOCIWarnEOFPICTUREFILEEstLogProbNUMPHENSRANDOMIZEfopen@@GLIBC_2.1RNormalALPHAPRIORBSetValue_IO_stdin_usedCORRBgenexpPrintKLDsprintf@@GLIBC_2.0FlikeFreqsInitializeSums__data_startPrintMembershipCheckPopPriorsrand@@GLIBC_2.0OutPutResultsOpenFile__gmon_start__strcpy@@GLIBC_2.0