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Adjust MAXSTR and recompile. %d %d %d %d %d %d Invalid %d_th line in pedfile: %s Correct format is: pedid id f_id m_id sex affect_status %d%d %d %d %dpedigree id = %d being used twice Error in the pedigrees Check file prest_errors file, and re-run the program %s %s Invalid line in chromfiles: %s %s Correct format is: marker_file genotype_file Unable to open marker_file %s Unable to open genotype_file %s Error reading num_mark from file %s %s %d %d Error in file %s: %s %lf Error of allele freq. in %d_th marker in file %s: Error in %s's %d_th marker sum of allele freq. = %f Error of marker spacing in file %s: %d markers, should be (%d - 1) spacings Spacing between adjacent markers should be in recombination fraction (theta), not in centi-Morgan Spacing cannot be negative value Error in marker data Check prest_errors file, and re-run the program %%%dd %%%dd %%%dd %%2d %%%dd NA %6.4f %6.4f %6.4f NA NA %7.5f %6.4f %6.4f %6.4f %6.4f %6.4f %6.4f NA %6.4f %6.4f %6.4f NA %7.5f %7.5f %6.4f %6.4f %6.4f %6.4f %7.5f %7.5f %7.5f %8.6f NA pedigree %d done Prest has detected Mendelian errors which are reported in the file prest_errors. In the current implementation of prest, the presence of Mendelian errors is not taken into account in the hypothesis testing. # Number of pedigrees: %d # Total number of individuals: # Number of chromosomes: # Total number of markers: # Number of markers on each chromosome %s: %5d # Number of genotyped pairs found in each of the # relationship categories analyzed by PREST: # (Note that unrelated pairs are checked within each pedigree.) Total: %d %7d full-sib pairs %7d half-sib pairs %7d grandparent-grandchild pairs %7d avuncular pairs %7d first-cousin pairs %7d unrelated pairs %7d half-avuncular pairs %7d half-first-cousin pairs %7d half-sib-plus-first-cousin pairs %7d parent-offspring pairs # Summary of genotyped pairs found in each pedigree pedid size f.sib h.sib g.p.c avun. f.cous. unrel. h.avun h.f.cous. h.sib+f.cous. p.o. Total %8d %4d %4d %8d # Number of pairs that have p-value of either EIBD or AIBS less than 0.2 # (for unrelated, p-value of IBS less than 0.2). # This is the number of pairs for which PREST would perform the MLRT. # (The MLRT will actually be performed only if option 2 is chosen.) # For each pair, performance of the MLRT, including 100,000 # simulated realizations takes approximately 5 minutes on # a Sun Ultra II with 360-MHz processor. # Number of pairs checked by MLRT %7d half-sib pairs In each pedigree # Assuming that there are not many misclassified relative pairs in the # data set and assuming that all the pairs are typed on roughly the # same markers (because which markers are typed affects the null means # of the AIBS and IBS statistics and affects the null variances of the # EIBD, AIBS and IBS statistics), then the sample averaged observed # statistics for each relationship type should not be significantly # different from what is expected. If they are significantly # different, if may indicate that the allele frequencies are not # accurately estimated, or that the assumptions of population # homogeneity and Hardy-Weinberg equilibrium are not appropriate. # It could also indicate a problem with the way the data are coded # (see item #7 in 'Tips' file). The following output contains # the information of sample summary of the statistics # obs = sample averaged observed statistic # mu(std) = sample averaged null mean (sample std. dev. of null mean) # (Note that the null mean of EIBD depends only on the null relationship, not on the data, so for EIBD # we give the null mean in place of the sample averaged null mean # std(std) = sample averaged standard deviation # (sample std. dev. of null standard deviation) # no.mark = sample averaged number of typed markers for a pair # (sample std. dev.) no.pairs no.mark(std) full-sib %7d NA( NA) full-sib %7d %6.1f(%6.1f) half-sib %7d NA( NA) half-sib %7d %6.1f(%6.1f) grandp-c %7d NA( NA) grandp-c %7d %6.1f(%6.1f) avuncular %7d NA( NA) avuncular %7d %6.1f(%6.1f) f-cousin %7d NA( NA) f-cousin %7d %6.1f(%6.1f) unrelated %7d NA( NA) unrelated %7d %6.1f(%6.1f) h-avuncular %7d NA( NA) h-avuncular %7d %6.1f(%6.1f) h-f-cousin %7d NA( NA) h-f-cousin %7d %6.1f(%6.1f) h-sib+f-cous %7d NA( NA) h-sib+f-cous %7d %6.1f(%6.1f) pa-offspring %7d NA( NA) pa-offspring %7d %6.1f(%6.1f) # Sample summary of EIBD obs mu std( std) full-sib NA NA NA( NA) full-sib %6.4f %6.4f %6.4f( NA) full-sib %6.4f %6.4f %6.4f(%8.6f) half-sib NA NA NA( NA) half-sib %6.4f %6.4f %6.4f( NA) half-sib %6.4f %6.4f %6.4f(%8.6f) grandp-c NA NA NA( NA) grandp-c %6.4f %6.4f %6.4f( NA) grandp-c %6.4f %6.4f %6.4f(%8.6f) avuncular NA NA NA( NA) avuncular %6.4f %6.4f %6.4f( NA) avuncular %6.4f %6.4f %6.4f(%8.6f) f-cousin NA NA NA( NA) f-cousin %6.4f %6.4f %6.4f( NA) f-cousin %6.4f %6.4f %6.4f(%8.6f) unrelated NA NA NA( NA) h-avuncular NA NA NA( NA) h-avuncular %6.4f %6.4f %6.4f( NA) h-avuncular %6.4f %6.4f %6.4f(%8.6f) h-f-cousin NA NA NA( NA) h-f-cousin %6.4f %6.4f %6.4f( NA) h-f-cousin %6.4f %6.4f %6.4f(%8.6f) h-sib+f-cousin NA NA NA( NA) h-sib+f-cousin %6.4f %6.4f %6.4f( NA) h-sib+f-cousin %6.4f %6.4f %6.4f(%8.6f) pa-offspring NA NA NA( NA) # Sample summary of AIBS obs mu( std) std( std) full-sib NA NA( NA) NA( NA) full-sib %6.4f %6.4f( NA) %6.4f( NA) full-sib %6.4f %6.4f(%8.6f) %6.4f(%8.6f) half-sib NA NA( NA) NA( NA) half-sib %6.4f %6.4f( NA) %6.4f( NA) half-sib %6.4f %6.4f(%8.6f) %6.4f(%8.6f) grandp-c NA NA( NA) NA( NA) grandp-c %6.4f %6.4f( NA) %6.4f( NA) grandp-c %6.4f %6.4f(%8.6f) %6.4f(%8.6f) avuncular NA NA( NA) NA( NA) avuncular %6.4f %6.4f( NA) %6.4f( NA) avuncular %6.4f %6.4f(%8.6f) %6.4f(%8.6f) f-cousin NA NA( NA) NA( NA) f-cousin %6.4f %6.4f( NA) %6.4f( NA) f-cousin %6.4f %6.4f(%8.6f) %6.4f(%8.6f) unrelated NA NA( NA) NA( NA) h-avuncular NA NA( NA) NA( NA) h-avuncular %6.4f %6.4f( NA) %6.4f( NA) h-avuncular %6.4f %6.4f(%8.6f) %6.4f(%8.6f) h-f-cousin NA NA( NA) NA( NA) h-f-cousin %6.4f %6.4f( NA) %6.4f( NA) h-f-cousin %6.4f %6.4f(%8.6f) %6.4f(%8.6f) h-sib+f-cousin NA NA( NA) NA( NA) h-sib+f-cousin %6.4f %6.4f( NA) %6.4f( NA) h-sib+f-cousin %6.4f %6.4f(%8.6f) %6.4f(%8.6f) pa-offsprin NA NA NA( NA) NA( NA) pa-offspring %6.4f %6.4f( NA) %6.4f( NA) pa-offspring %6.4f %6.4f(%8.6f) %6.4f(%8.6f) # Sample summary of IBS f -cousin %6.4f %6.4f( NA) %6.4f( NA) unrelated %6.4f %6.4f( NA) %6.4f( NA) unrelated %6.4f %6.4f(%8.6f) %6.4f(%8.6f) h-avuncular %6.4f %6.4f( NA) %6.4f( NA) h-avuncular %6.4f %6.4f(%8.6f) %6.4f(%8.6f) pa-offsprin NA NA( NA) NA( NA) pa-offspring %6.4f %6.4f( NA) %6.4f( NA) pa-offspring %6.4f %6.4f(%8.6f) %6.4f(%8.6f) {Gz?$@???ffffff?j@j@errors in pedigree %d: %d'th parents have the same id individual id = %d being used %d has two genders pedigree %d is not complete: %d's parents: %d and/or %d do not have their parent's ids Error reading genotype data for %d in ped %d at %s at line %d Error reading genotype data for %d in ped %d at %s Genotyping errors: pedigree %d, at %s's %dth marker %d's genotypy is %d %d no. of alleles of this marker is %d Warning: The length of the %d_th line in file %s Mendelian errors: pedigree %d at %s's %dth marker %d's parents are %d %d, and genotype: %d %d %d %d %d %d %d's parents are %d %d, and genotype: @@@@@@@UUUUUU?UUUUUU???@@@@@@@UUUUUU?UUUUUU????@Ͼ%:\ ?!Q?qOOKu?Y/?fTրcJ.F?(V?7 J?VD$`?0z?]pprogram is wrong for EIBD @ @@MbP??@ @@ @@@ @@?@ @>٬\?@d`?A@d`?A?j@Y@??@ @Y@??{Gz?{Gz??p????????????????????i???????????ܢ6FVfvƆֆ&6FVfv  [(  t@8ooo0dd(<7f)u7\v2\p)j~)U9p(;)o$B?) -!E"[#r%&1234 5 68 8Q 9k ; = > ? @ A B! C8 DQ Eh F G H I N Q' RA SY Tr V Y o r u# {= |Z w  # @ Z F   3"rO3;BE8vRY]1nkXspx) #$%& "dinit.c/usr/src/bs/BUILD/glibc-2.1/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-2.1/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)=(0,3)__blkcnt64_t:t(15,45)=(15,6)__fsblkcnt_t:t(15,46)=(15,4)__fsblkcnt64_t:t(15,47)=(15,5)__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)01.0101.0101.0101.0101.0101.01.symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.got.rel.plt.init.plt.text.fini.rodata.data.eh_frame.ctors.dtors.got.dynamic.bss.stab.stabstr.comment.note# 1((7 ?"Go6ToPc 88l @@ u/{  p,[[4  ``ddlltthܢg D 0.nn/x/h5? =K(8@    [ [`dltܢn  "  -Ġ1l?ȠK a`t  0 ̠d" [ [ h[ `p` [  @  (@:@H`]T@T_ X03"h tܢ}X [@t"S? LU  P$$i `" 5 $ *ps<0Q LO ZU) b hZ pR"<   $Tq "  X ,  A "P  $ІRA4j JV@Q [xZ Q  n 8  )[ PSJ Re .  T"/"+ 9 I|m V0$hot@"$ P S Py) [ `$U  pX(E  2P < 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__prest.cp012.280countmlrt.281checkmarker.282checkallefreq.283numinlist.302anclist.305cp0feof@@GLIBC_2.0findpedgeno_DYNAMICgetibd2_etext__register_frame_info@@GLIBC_2.0inbred_checkcrossover_new_fp_hwforEIBDvarfprintf@@GLIBC_2.0get3statfflush@@GLIBC_2.0transproballsimugeno1geno2pnormrewind@@GLIBC_2.0check_avuncularcheck_halfsibcombine_initgetibd1malloc@@GLIBC_2.0get3statandmustdfscanf@@GLIBC_2.0mapthetatocm__deregister_frame_info@@GLIBC_2.0transprobfindrelationchecktime@@GLIBC_2.0_startfgets@@GLIBC_2.0EMforp012__strtol_internal@@GLIBC_2.0recoding__bss_startmain__libc_start_main@@GLIBC_2.0getibd0build_anclistcheck_halfavuncularcheck_anclistdata_startprintf@@GLIBC_2.0_finicp2fclose@@GLIBC_2.1check1_anclistcheck_halfpluscousincheck_halfcousinsrand@@GLIBC_2.0forIBSvarexit@@GLIBC_2.0check_cousinsscanf@@GLIBC_2.0_edata_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endcheck_grandpccp1fopen@@GLIBC_2.1forAIBSvar_IO_stdin_usedfp_errorsprintf@@GLIBC_2.0mapcmtotheta__data_startrand@@GLIBC_2.0getapprloglikelihoodcheckMend__gmon_start__