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zEHt u$e[^_]ÉUWVSEE]M Ev]|ډU D0EU;T4ËMfContig%d %cCO Contig%d %d %d %d %c BQ %sBS %d %d %s >RD AF %d 0 0 QA %d %d %d %d DS %c %d %s.%s.contigs.links%-60s %3d Cannot open %s.Usage: %s File_of_reads [options] File_of_reads is a file of DNA reads in FASTA format If the file of reads is named 'xyz', then the file of quality values must be named 'xyz.qual', and the file of constraints named 'xyz.con'. -a N specify band expansion size N > 10 (20) -b N specify base quality cutoff for differences N > 15 (20) -c N specify base quality cutoff for clipping N > 5 (12) -d N specify max qscore sum at differences N > 20 (200) -e N specify clearance between no. of diff N > 10 (30) -f N specify max gap length in any overlap N > 1 (20) -g N specify gap penalty factor N > 0 (6) -h N specify max overhang percent length N > 2 (20) -m N specify match score factor N > 0 (2) -n N specify mismatch score factor N < 0 (-5) -o N specify overlap length cutoff > 20 (40) -p N specify overlap percent identity cutoff N > 65 (80) -r N specify reverse orientation value N >= 0 (1) -s N specify overlap similarity score cutoff N > 400 (900) -t N specify max number of word matches N > 30 (300) -u N specify min number of constraints for correction N > 0 (3) -v N specify min number of constraints for linking N > 0 (2) -w N specify file name for clipping information (none) -x N specify prefix string for output file names (cap) -y N specify clipping range N > 5 (250) -z N specify min no. of good reads at clip pos N > 0 (3) Each option must begin with a dash (-)An integer value is expected for each option except -x and -w.Value for band expansion size must be > 10Value for base quality cutoff for differences is between 16 and 99Value for base quality cutoff for clipping is between 6 and 99Value for max qscore sum at differences must be >= 20Value for clearance between no. of diff must be > 10Value for max gap length in any overlap must be > 1Value for gap penalty factor must be > 0Overhang percent length must be > 2Value for match score factor must be > 0Value for mismatch score factor must be < 0Value for overlap length cutoff must be > 20Value for overlap percent identity cutoff must be > 65Value for reverse orientation must be >= 0Value for overlap similarity score cutoff must be > 400Value for max number of word matches must be > 30Value for min number of constraints for correction must be > 0Value for min number of constraints for linking must be > 0A file name is expected for the -w optionA prefix string is expected for the -x optionValue for clipping range must be > 5Value for min no. of good reads at clip pos must be > 0Number of iterations for checking constraints: %d No file of quality values (.qual) is found File of quality values is short or wrong in formatSeq name and its .qual name are different for fragment: %s Short of quality values for fragment: %s Quality values not between 0 and 99 for fragment: %s No file of constraints (.con) is found. constraint error: format is wrongconstraint error: min distance is larger than maxconstraint error: min distance is negativeconstraint error: no fragment has name %squalcutoff is not between 0 and 99Pair of identical reads: %s and %s The number of similar pairs of reads processed: %ld The amount of space requested : %ld Number of segment pairs = %ld; number of pairwise comparisons = %ld '+' means given segment; '-' means reverse complement File for clipping information: format is wrongFile for clipping information: values are out of rangeClipping file: no read has name %sUpdateLeftCV: nonpositive valueUpdateRightCV: nonpositive valueNo overlap is found in the given 5' clipping range for read %s 5' clipping ranges for overlaps: No overlap is found in the given 3' clipping range for read %s 3' clipping ranges for overlaps: Chimera: %s at base %d with %d left and %d right poor overlaps Number of overlaps removed: %d qualscore %5d score %6d identity %4.2ferri %4.2f errj %4.2f error %4.2flengths of diffs and sims: %s left %d %s right %d middle %dOverlap %s%c and %s%c %c %s The same fragment found in MergeContigs%15s %15s %9d %9d %dth link between %s%c and %s%c %-12s %-12s %6d %6d %dth link between %s%c and %s%c %d constraints between %s%c and %s%c Secondary join made between %s%c and %s%c ******************* Contig %d ******************** The array RDstm runs out of boundProduceFlatOut: unexpected length of padded readClip %s left clip: %d, right clip: %d, length: %d, right size %d An error occurred in construction of an alignment for a contig because the ends of read %s or its neighbors are not sufficiently trimmed. The -w option could be used to trim the reads more aggressively.DiffQual: maxlen is not large enoughMergeQual: maxlen is not large enough Overlaps Containments No. of Constraints Supporting Overlap The contigs above and below are linked by %d constraints. Contig%d and Contig%d are linked by %d constraints. %s is in %s A low or up diagonal is out of rangeRan out of memory: %ld bytes requested. Y@333333?<h4444Dp4Ќ(T <<<<<<<<<<<<<<<<܏<<<<<<<<<<<<̏< <<<,<<<<<<<<<<<<B`(L?z> ,d, 8 (@Ё do`oo0fvƅօ&6FVfvdd9<Hr0,V1V cV$[Lby !"#3%K&a1x234568 9";B=X>n?@ABCDE F$G;HTIiNQRST9UUVmX[^ehl q r5 uP vm y z } & @ ˔t F  #V Y 4u < C F S Z ^ltMyn4 Lb8wbKL#5LwH8KgLUZ^?awb\r5 7!899S:m dinit.c/usr/src/build/87998-i386/BUILD/glibc-2.2.5/csu/gcc2_compiled.int:t(0,1)=r(0,1);-2147483648;2147483647;char:t(0,2)=r(0,2);0;127;long int:t(0,3)=r(0,3);-2147483648;2147483647;unsigned int:t(0,4)=r(0,4);0000000000000;0037777777777;long unsigned int:t(0,5)=r(0,5);0000000000000;0037777777777;long long int:t(0,6)=@s64;r(0,6);01000000000000000000000;0777777777777777777777;long long unsigned int:t(0,7)=@s64;r(0,7);0000000000000;01777777777777777777777;short int:t(0,8)=@s16;r(0,8);-32768;32767;short unsigned int:t(0,9)=@s16;r(0,9);0;65535;signed char:t(0,10)=@s8;r(0,10);-128;127;unsigned char:t(0,11)=@s8;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);8;0;complex double:t(0,17)=r(0,17);16;0;complex long double:t(0,18)=r(0,18);24;0;__builtin_va_list:t(0,19)=*(0,20)=(0,20)../include/libc-symbols.h/usr/src/build/87998-i386/BUILD/glibc-2.2.5/build-i386-linux/config.h../sysdeps/gnu/_G_config.h../sysdeps/unix/sysv/linux/bits/types.h../include/features.h../include/sys/cdefs.h../misc/sys/cdefs.h/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/stddef.hsize_t:t(8,1)=(0,4)__u_char:t(4,1)=(0,11)__u_short:t(4,2)=(0,9)__u_int:t(4,3)=(0,4)__u_long:t(4,4)=(0,5)__u_quad_t:t(4,5)=(0,7)__quad_t:t(4,6)=(0,6)__int8_t:t(4,7)=(0,10)__uint8_t:t(4,8)=(0,11)__int16_t:t(4,9)=(0,8)__uint16_t:t(4,10)=(0,9)__int32_t:t(4,11)=(0,1)__uint32_t:t(4,12)=(0,4)__int64_t:t(4,13)=(0,6)__uint64_t:t(4,14)=(0,7)__qaddr_t:t(4,15)=(4,16)=*(4,6)__dev_t:t(4,17)=(4,5)__uid_t:t(4,18)=(4,3)__gid_t:t(4,19)=(4,3)__ino_t:t(4,20)=(4,4)__mode_t:t(4,21)=(4,3)__nlink_t:t(4,22)=(4,3)__off_t:t(4,23)=(0,3)__loff_t:t(4,24)=(4,6)__pid_t:t(4,25)=(0,1)__ssize_t:t(4,26)=(0,1)__rlim_t:t(4,27)=(4,4)__rlim64_t:t(4,28)=(4,5)__id_t:t(4,29)=(4,3)__fsid_t:t(4,30)=(4,31)=s8__val:(4,32)=ar(4,33)=r(4,33);0000000000000;0037777777777;;0;1;(0,1),0,64;;__daddr_t:t(4,34)=(0,1)__caddr_t:t(4,35)=(4,36)=*(0,2)__time_t:t(4,37)=(0,3)__useconds_t:t(4,38)=(0,4)__suseconds_t:t(4,39)=(0,3)__swblk_t:t(4,40)=(0,3)__clock_t:t(4,41)=(0,3)__clockid_t:t(4,42)=(0,1)__timer_t:t(4,43)=(0,1)__key_t:t(4,44)=(0,1)__ipc_pid_t:t(4,45)=(0,9)__blksize_t:t(4,46)=(0,3)__blkcnt_t:t(4,47)=(0,3)__blkcnt64_t:t(4,48)=(4,6)__fsblkcnt_t:t(4,49)=(4,4)__fsblkcnt64_t:t(4,50)=(4,5)__fsfilcnt_t:t(4,51)=(4,4)__fsfilcnt64_t:t(4,52)=(4,5)__ino64_t:t(4,53)=(4,5)__off64_t:t(4,54)=(4,24)__t_scalar_t:t(4,55)=(0,3)__t_uscalar_t:t(4,56)=(0,5)__intptr_t:t(4,57)=(0,1)__socklen_t:t(4,58)=(0,4)../linuxthreads/sysdeps/pthread/bits/pthreadtypes.h../sysdeps/unix/sysv/linux/bits/sched.h__sched_param:T(10,1)=s4__sched_priority:(0,1),0,32;;_pthread_fastlock:T(9,1)=s8__status:(0,3),0,32;__spinlock:(0,1),32,32;;_pthread_descr:t(9,2)=(9,3)=*(9,4)=xs_pthread_descr_struct:__pthread_attr_s:T(9,5)=s36__detachstate:(0,1),0,32;__schedpolicy:(0,1),32,32;__schedparam:(10,1),64,32;__inheritsched:(0,1),96,32;__scope:(0,1),128,32;__guardsize:(8,1),160,32;__stackaddr_set:(0,1),192,32;__stackaddr:(0,19),224,32;__stacksize:(8,1),256,32;;pthread_attr_t:t(9,6)=(9,5)pthread_cond_t:t(9,7)=(9,8)=s12__c_lock:(9,1),0,64;__c_waiting:(9,2),64,32;;pthread_condattr_t:t(9,9)=(9,10)=s4__dummy:(0,1),0,32;;pthread_key_t:t(9,11)=(0,4)pthread_mutex_t:t(9,12)=(9,13)=s24__m_reserved:(0,1),0,32;__m_count:(0,1),32,32;__m_owner:(9,2),64,32;__m_kind:(0,1),96,32;__m_lock:(9,1),128,64;;pthread_mutexattr_t:t(9,14)=(9,15)=s4__mutexkind:(0,1),0,32;;pthread_once_t:t(9,16)=(0,1)_pthread_rwlock_t:T(9,17)=s32__rw_lock:(9,1),0,64;__rw_readers:(0,1),64,32;__rw_writer:(9,2),96,32;__rw_read_waiting:(9,2),128,32;__rw_write_waiting:(9,2),160,32;__rw_kind:(0,1),192,32;__rw_pshared:(0,1),224,32;;pthread_rwlock_t:t(9,18)=(9,17)pthread_rwlockattr_t:t(9,19)=(9,20)=s8__lockkind:(0,1),0,32;__pshared:(0,1),32,32;;pthread_spinlock_t:t(9,21)=(0,1)pthread_barrier_t:t(9,22)=(9,23)=s20__ba_lock:(9,1),0,64;__ba_required:(0,1),64,32;__ba_present:(0,1),96,32;__ba_waiting:(9,2),128,32;;pthread_barrierattr_t:t(9,24)=(9,25)=s4__pshared:(0,1),0,32;;pthread_t:t(9,26)=(0,5)wchar_t:t(11,1)=(0,3)wint_t:t(11,2)=(0,4)../include/wchar.h../wcsmbs/wchar.h../sysdeps/unix/sysv/linux/i386/bits/wchar.h__mbstate_t:t(13,1)=(13,2)=s8__count:(0,1),0,32;__value:(13,3)=u4__wch:(11,2),0,32;__wchb:(13,4)=ar(4,33);0;3;(0,2),0,32;;,32,32;;_G_fpos_t:t(3,1)=(3,2)=s12__pos:(4,23),0,32;__state:(13,1),32,64;;_G_fpos64_t:t(3,3)=(3,4)=s16__pos:(4,54),0,64;__state:(13,1),64,64;;../include/gconv.h../iconv/gconv.h :T(17,1)=e__GCONV_OK:0,__GCONV_NOCONV:1,__GCONV_NODB:2,__GCONV_NOMEM:3,__GCONV_EMPTY_INPUT:4,__GCONV_FULL_OUTPUT:5,__GCONV_ILLEGAL_INPUT:6,__GCONV_INCOMPLETE_INPUT:7,__GCONV_ILLEGAL_DESCRIPTOR:8,__GCONV_INTERNAL_ERROR:9,; :T(17,2)=e__GCONV_IS_LAST:1,__GCONV_IGNORE_ERRORS:2,;__gconv_fct:t(17,3)=(17,4)=*(17,5)=f(0,1)__gconv_init_fct:t(17,6)=(17,7)=*(17,8)=f(0,1)__gconv_end_fct:t(17,9)=(17,10)=*(17,11)=f(0,20)__gconv_trans_fct:t(17,12)=(17,13)=*(17,14)=f(0,1)__gconv_trans_context_fct:t(17,15)=(17,16)=*(17,17)=f(0,1)__gconv_trans_query_fct:t(17,18)=(17,19)=*(17,20)=f(0,1)__gconv_trans_init_fct:t(17,21)=(17,22)=*(17,23)=f(0,1)__gconv_trans_end_fct:t(17,24)=(17,25)=*(17,26)=f(0,20)__gconv_trans_data:T(17,27)=s20__trans_fct:(17,12),0,32;__trans_context_fct:(17,15),32,32;__trans_end_fct:(17,24),64,32;__data:(0,19),96,32;__next:(17,28)=*(17,27),128,32;;__gconv_step:T(17,29)=s56__shlib_handle:(17,30)=*(17,31)=xs__gconv_loaded_object:,0,32;__modname:(17,32)=*(0,2),32,32;__counter:(0,1),64,32;__from_name:(4,36),96,32;__to_name:(4,36),128,32;__fct:(17,3),160,32;__init_fct:(17,6),192,32;__end_fct:(17,9),224,32;__min_needed_from:(0,1),256,32;__max_needed_from:(0,1),288,32;__min_needed_to:(0,1),320,32;__max_needed_to:(0,1),352,32;__stateful:(0,1),384,32;__data:(0,19),416,32;;__gconv_step_data:T(17,33)=s36__outbuf:(17,34)=*(0,11),0,32;__outbufend:(17,34),32,32;__flags:(0,1),64,32;__invocation_counter:(0,1),96,32;__internal_use:(0,1),128,32;__statep:(17,35)=*(13,1),160,32;__state:(13,1),192,64;__trans:(17,28),256,32;;__gconv_info:T(17,36)=s8__nsteps:(8,1),0,32;__steps:(17,37)=*(17,29),32,32;__data:(17,38)=ar(4,33);0;-1;(17,33),64,0;;__gconv_t:t(17,39)=(17,40)=*(17,36)_G_iconv_t:t(3,5)=(3,6)=u44__cd:(17,36),0,64;__combined:(3,7)=s44__cd:(17,36),0,64;__data:(17,33),64,288;;,0,352;;_G_int16_t:t(3,8)=(0,8)_G_int32_t:t(3,9)=(0,1)_G_uint16_t:t(3,10)=(0,9)_G_uint32_t:t(3,11)=(0,4)_IO_stdin_used:G(0,1)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)GCC: (GNU) 2.96 20000731 (Red Hat Linux 7.3 2.96-110)01.0101.0101.0101.0101.0101.0101.01.symtab.strtab.shstrtab.interp.note.ABI-tag.hash.dynsym.dynstr.gnu.version.gnu.version_r.rel.dyn.rel.plt.init.text.fini.rodata.data.eh_frame.dynamic.ctors.dtors.got.bss.stab.stabstr.comment.note# 1((7 Ёp?@@Go00.To``0c l  u88pPP0{ "" PPPTTQ\\QddQXQ Q dYrhtt\z  | (Ё@0` 8 P   T\d " 2І =A\O [І q0 @ p T2` ` X `  (1 8$D(K,T0_4o8x<@DHLPTX\dhlptx |"(/|4;>ADGIMQUY^`bglqv|3@3,$(0x 8$42<=EMU ^gqt} D@ `hlpt x|!)/9CEHOW^elsy`d   80 !`% - 7 Eg3 V e n x( b ,N L  {  Ms `"| p%!(h4 4;-N X^pc \ u6  8$ 4b ` \a \  \w  | ]n  i G1 +pg 4 <8 B[R LTpf sD -  %"$3    %  Ѕ@+ ;DXG U]e# pPG }ks  <  HF ;   @  Դ  d-K $  / u ? 2Q  W |h g \E u  |  8 \ H ` plR   X7 -  0 d- @= B 9 L a 7 i N  r  { l P 8_ Ģ  j  T(  `-      ! p5 d @ ĿA G  S t Y ^ X4 m  init.cinitfini.cgcc2_compiled.call_gmon_startcrtstuff.cp.0__DTOR_LIST__completed.1__do_global_dtors_aux__EH_FRAME_BEGIN__fini_dummyobject.2frame_dummyinit_dummyforce_to_data__CTOR_LIST____do_global_ctors_aux__CTOR_END____DTOR_END____FRAME_END__cap3.cmatchmismatchover_lenper_centminsatniterationsgapfacchimratequalcutoffqualscorecutoffminlinkscutoffscoreclearancehalfbdwidthextrapenclipqualmidqualcliplengthclipdepthgapmaxlencutoffrevortoosimdifacfrlimitforesconreads_numallmemfnprefixistherequalinfopfrsizezeromaxlenCCDDRRSSSat5at3bt5bt3vertvqtopibotitopjbotjSCORESTARISTARJENDIENDJSBANDfragname1fragname2cbufferleftcvecrightcveccbuggersapplastno_misno_matal_lenERR5ERR3qualscoregapmaxlenCoveragereadcountminusreadcountpluscgstrandidbufsizealgbuf1algbuf2qualbuf1qualbuf2frgapsizecontigs_numqrepinprocrepinproqdelprocdelproFp_AFFp_RDAAQAAfilter.cqscorecutoffdnalenaalennumestwordsizedistancenumchainsfcutofficutoffantidisaaoverqgaplenlgaplenmismhsimcutoffidncutoffDDNframe1frameptframe2frame3frame4dnals4tsizetablelistrqpaylpayinitsdiff8PPNcfm1diagonalsegsizesegpairsegstdtuplistestdidnals2nncodeposcutpsizednals3tupsizecseglendawfdstCalClipWithQualJoinContigsTryToJoinEvaluateConstBandedLocalAlignComputeOverlapContmentComputeDaChainSegbig_pass_DYNAMICMergeContigsMatchFiveThreeComputeAiDiIsSameCloneNameAnyLappMoreSpacefpoint__register_frame_info@@GLIBC_2.0TryOneEndstrcmp@@GLIBC_2.0_fp_hwTagPolyBasefrgapsfprintf@@GLIBC_2.0GetErRateolistfflush@@GLIBC_2.0ComputDistForContigsFindBestBandedDiffDoubleSegSpaceDoContainedfrlistCutJoinCloseIsRtStrandFINDLAPPFreeSpaceUpdateLeftCVCompErrorJOINPresentLayoutSetUpWCopynameAddToAlignSEPARATEfrscore_initMergeQualSpeedUpmalloc@@GLIBC_2.0FindPolyBaseComputeFRScorefscanf@@GLIBC_2.0FormContigLinks__deregister_frame_info@@GLIBC_2.0tpointstderr@@GLIBC_2.0fatalfweighttableCheckConst2Filterfatalupdiag_startfgets@@GLIBC_2.0CopyContainedFgfragpredFinalizeClippinglowdiagsegmentUpdateDistAddContainedScoreTerminalGapsSetUpFilterCheckConstLAPPcontigs2fragtailDoClipping__bss_startmain__libc_start_main@@GLIBC_2.0TellOverlapProduceFlatOutUpdateRightCVShowdata_startEvaluateOverlapprintf@@GLIBC_2.0_finiTakeOutContigs2EnterIntoWorkfclose@@GLIBC_2.1CopynameorientINITReadConstraintsMAKEIdentifyChimeraswordcountoffdiffexit@@GLIBC_2.0ckopensscanf@@GLIBC_2.0_edata_IO_putc@@GLIBC_2.0_GLOBAL_OFFSET_TABLE_free@@GLIBC_2.0_endQuickSort__ctype_b@@GLIBC_2.0CompareDiffQualMoveContAskBufSpacefopen@@GLIBC_2.1RemovePoorOverlaps_IO_stdin_usedseg_numckallocReadQualBuildBridgesprintf@@GLIBC_2.0MakeOverlapList2__data_startcontigsFindHead_IO_getc@@GLIBC_2.0LocalAlignIsGoodComputeDistASSEMworkComputeConDistInitializeClipping__gmon_start__