It's the xxxxxxxx's change them to nnnnnnn's and it converted fine On 02/11/2012, at 12:57 PM, Robert Trygve Good wrote: Here's another one just to make sure it wasn't specific to one assembly Generated 3 unique template ids for 3 valid reads. Error while dumping Tridacna_squamosa_rep_c670. Internal logic/programming/debugging error (*sigh* this should not have happened). Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/ "Read does not cover given contigposition" ->Thrown: char Contig::getQualityInRead(int32 contigposition, int32 readindex) ->Caught: void dumpContigs(list<Contig> & clist, ostream & fout) Aborting process, probably due to an internal error. Cheers Rob CO Tridacna_squamosa_rep_c670 NR 3 LC 828 CT H454 2 2 = . Note=Smoking gun Edit: A PL: 0 RS: 12 RL: 1 RWTS: 0 EL: 1 CT H454 23 23 = . Note=No edit. PL: 1 RS: 7 RL: 0 RWTS: 0 EL: 0 CT H454 31 31 = . Note=No edit. PL: 3 RS: 7 RL: 0 RWTS: 0 EL: 0 CT H454 96 96 = . Note=No edit. PL: 0 RS: 4 RL: 0 RWTS: 0 EL: 0 CT IUPc 622 622 = . Note=Strain 'StrainX': Y CT IUPc 638 638 = . Note=Strain 'StrainX': Y CT H454 697 697 = . Note=No edit. PL: 0 RS: 2 RL: 1 RWTS: 0 EL: 1 CT DGPc 757 757 = . Note=*: 1 A: 1 - 50%25 CT H454 757 757 = . Note=No edit. PL: 1 RS: 1 RL: 0 RWTS: 0 EL: 0 CT DGPc 786 786 = . Note=*: 1 C: 1 - 50%25 CT H454 786 786 = . Note=No edit. PL: 3 RS: 1 RL: 0 RWTS: 0 EL: 0 CS gaccttgaaccttgatatttggtatttatctttattgtagacctttgctgcttggtactcaggtgagcgatataggaccatcaxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxgtgtaccccaaggatgtattctctctgttacacttttcagtgtaaaaataaacagtatagttaaagctatctgtcctggtgtagactgttccctctatgttgatgacttcgttatatgcttcagatctcgaaatatgaatattattgagagacaacttcaacagtgtctcaacaaattgcaaacatggtctgatgaaaatggcttcagattttcaaagtccaaaactaagtgcatgcacctctgtaatctacgaggtattcacccagatcctgaactgtatttggacaaaactaaaattgaagtcgtgtccgagtttaaatttcttggagtcatctttgacagaaagctttccttcyttcctcacatcactgyacttaaaaagaagtgcaagaaggctcttaatcttcttaaggttgtggcccattctgaa*tggggagcagaccgtaaagtcctcttgcgactttatcggtctttagttcgctccaaatt*gattatggatctgttgtatacggatcgg*ccgtaaatcctatctgaaaattctcgattctatacaccacga CQ 7/..99:2444<<<<9?;==DBAA;;;A<<111448<>???>@455:====AAAABAAAAECDFFDDBBDDDDD::668EEEC!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!IIIIICCCCIIIIIIIIIIIIIIIIIIIIIIIICCB@IIIIIB66633F:::GCIIIIIIIIFFFIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIJJDCCLLLLLLMMMMMMMMLMMMMKKIIKMMMMMMLLLKIIIIILKKKKLLLIIIIKKKLLLLLLLLLLKKKLLLLKKKLLLLLIIILLKLBBBBIIGIKLKIIIDDDDLKKGGILLB???HI>>JIIIIIIIJIIIIILKIIIIILLLLLLLLLLLLIIIKKLIIILJIIIIIIGCBBLLKKCCCCIE7777FFBBBFFGIIIILLJJC88>EEE<<<F=>GGIGGGEDC<55:?A>>2119;<<<??=?C:DDAAAFFB@A??CDE@FGGG66666G55C<;<AFFFFDDFCCCFFFCDCEEEEEEEEEEEBBB@@@;;;EEF<<"<<>>@E4;;;DDDDD>>>>>443=<88888<8;;>7:///88883/--88888;88844"38@?>>888>@B@<<<664496646:--"---26669::5656562222::----222246..07744--- \\ RD HDIEH6T02GHTAM RG 1 RS gactacgagtagactATGATGGTCCTATATCGCTCACCTGAGTACCAAGCAGCAAAGGTCTACAATAAAGATAAATACCAAATATCAAGGTTCAAGGTCTAAATGataatgaaacaagagcagcaatttgtcgccaatttgacttgagtacttgaagttccattccagacaagcaagtaatacgtgtaagatgaagatacaaagtggaaatttaaataaacttcgacacgttaaggtagaagtttattgtttcttgcgtaaattgtaactctagtaatattgcaacaactatgcataacctaagtttggaagtcgttctgacttgagtatgactaaagttatattccagacaggcctataaangctagtaaaatgacattcaaaagggtaataactcaaagacagacacgaaattagagttacaatttctgtcgcactagctacttaccaaatatttcgactaaaccaaagttaactactaactaacccccttaatttttacaaacggttcctaattttacccttaacgttaaggtaacttaggaaaccttaaaaggttttttacgaacgtttacccggggaactaaaacggccgaaaaaaggaaaggtttaccttaaaccgggtccggtttgggggttacccgggtttcccgg RQ FFFFFFFFFFFFFFFFCEEE866::DDDDDBBDDFFDCEAAAABAAAA====:554@>???><844111<<A;;;AABD==;?9<<<<4442:99../76...9:7759<4..0004<<???AABD??CFA?:::AA<;999766:////42242666666799;;:4348444444488AA??AA?8443444442434666=:55113,,,,,,,,,,.57-..--2.----5551,--2,,,,,,.,,,.,.33--,,,117677:===33422....335--,,271577331111-,,3111----5779666../.;>?9444444<<866<;;9.//...38999-----35100!33,,,,,,,,477700,,,,,,,,,3//500,,,.66,,,47474,,,,,,,,,06,,,311,,,,,,,,.341310,,,1,,,.....0,,,,,,3.0.....---22200766444.,,,,,,,,,..,,,,,,,,0//,,,,,,,,,,,,,,,.,,,)),,,,..,,,,,..0...,,,,,,,,,,,--44//22,,)0,,,,,,,,..//..,,,,,,,,,,,,,,,.,,22,---)))44633-222231100643000,,.,-,,,,,,,0000))),,,,,,,, TN HDIEH6T02GHTAM SL 17 SR 105 QR 99 RT HAF7 17 45 = MIRA . RT HAF6 46 50 = MIRA . RT HAF5 51 97 = MIRA . RT HAF3 98 99 = MIRA . ER AT 83 1 17 99 RD HDIEH6T02HR338 RG 1 RS gactacgagtagactGGTGTACCCCAAGGATGTATTCTCTCTGTTACACTTTTCAGTGTAAAAATAAACAGTATAGTTAAAGCTATCTGTCCTGGTGTAGACTGTTCCCTCTATGTTGATGACTTCGTTATATGCTTCAGATCTCGAAATATGAATATTATTGAGAGACAACTTCAACAGTGTCTCAACAAATTGCAAACATGGTCTGATGAAAATGGCTTCAGATTTTCAAAGTCCAAAACTAAGTGCATGCACCTCTGTAATCTACGAGGTATTCACCCAGATCCTGAACTGTATTTGGACAAAACTAAAATTGAAGTCGTGTCCGAGTTTAAATTTCTTGGAGTCATCTTTGACAGAAAGCTTTCCTTCTTTCCTCACATCACTGTACTTAAAAAGAAGTGCAAGAAGGCTCTTAATCTTCTTAAGGTTGTGGCCCATTCTGAA*TGGGGAGCAGACCGtaaagtcctcttgcgacttatagtctacgcgtggtcggcgtctctcaaggcacgcaggggataggnn RQ IIIIIIIIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIIIIIIIICCB@IIIIIB66633F:::GCIIIIIIIIFFFIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIICBBFHHFFFIIIIIIIIIIIIIHFFFHIIIIIIIIIHFFFFFIHHHHIIIFFFFHHHIIIIIIIIIIHHHIIIIHHHIIIIIFFFIIHI@@@@DDDFHIHFFFBBBBIHHDDFII@=<<:?<<GBBCC@@@G@@@B@IH@@@@DIIIIIIIIIIII@@@HHIDDDIGDDDDDDD@@@IIIIBBBBHD6666DD@@@DDDFFFFIIGG666<BBB---;9<DDD?AAA::0//9=?;91//0922222--.268;>7=>4455545CCDDDD44444B11@:455::8;@@C>>99::=A=2---22220,,,14...32234;86"722229.93302.-.--377997478:863....8:;:97;:;:1....344449444613222930303....73/00!! TN HDIEH6T02HR338 SL 17 SR 462 QR 527 AO 1 447 1 447 AO 449 529 448 528 RT HAF5 17 273 = MIRA . RT SRMr 129 129 = MIRA . RT SRMr 180 180 = MIRA . RT SRMr 224 224 = MIRA . RT SRMr 258 258 = MIRA . RT SRMr 274 274 = MIRA . RT HAF3 274 279 = MIRA . RT SRMr 279 279 = MIRA . RT HAF5 280 323 = MIRA . RT SRMr 294 294 = MIRA . RT SRMr 298 298 = MIRA . RT HAF3 324 324 = MIRA . RT SRMr 324 324 = MIRA . RT HAF5 325 372 = MIRA . RT SRMr 327 327 = MIRA . RT SRMr 369 369 = MIRA . RT HAF5 390 462 = MIRA . RT SRMr 438 438 = MIRA . ER AT 266 711 17 462 RD HDIEH6T01AXT54 RG 1 RS gactacgagtagactGTTGATGACTTCGTTATATGCTTCAGATCTCGAAATATGAATATTATTGAGAGACAACTTCAACAGTGTCTCAACAAATTGCAAACATGGTCTGATGAAAATGGCTTCAGATTTTCAAAGTCCAAAACTAAGTGCATGCACCTCTGTAATCTACGAGGTATTCACCCAGATCCTGAACTGTATTTGGACAAAACTAAAATTGAAGTCGTGTCCGAGTTTAAATTTCTTGGAGTCATCTTTGACAGAAAGCTTTCCTTCCTTCCTCACATCACTGCACTTAAAAAGAAGTGCAAGAAGGCTCTTAATCTTCTTAAGGTTGTGGCCCATTCTGAA*TGGGGAGCAGACCGTAAAGTCCTCTTGCGACTTTATCGGTCTTTAGTTCGCTCCAAATT*GATTATGGATCTGTTGTATACGGATCGG*CCGTAAATCCTATCTGAAAATTCTCGATTCTATACACCACGAagtctgcgtnttgtccttggagcattcagaacttctcccgtcaatagttc RQ FFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIHH@@?IIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFFFFFFFFF:::8FFDDDDDDFF===;D???DAAA====FF;;DFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFD?==BA>>00..34----9678889@@AAAAABDA666???;;;D;;CCFDDDBBA;4449<<<00089;;;>><>BBBB???DDA??==BB===ABB55555D44?:::?DDDDAAAAAADDDAAADDDDDDDDDDDAAA???:::DDD::":;==?D3:::DDDDD>>>>>443=<88888<8;;>7:///88883/--88888;88844"38@?>>888>@B@<<<664496646:--"---26669::5656562222::----222246..07744---,,24430.0!,,0,,,,,,,,,,00000,,,,,0.../23.,0,,,,,,0 TN HDIEH6T01AXT54 SL 17 SR 480 AO 1 348 1 348 AO 350 408 349 407 AO 410 437 408 435 AO 439 530 436 527 RT HAF5 17 174 = MIRA . RT SRMr 30 30 = MIRA . RT SRMr 81 81 = MIRA . RT SRMr 125 125 = MIRA . RT CRMr 126 126 = MIRA . RT SRMr 159 159 = MIRA . RT SRMr 175 175 = MIRA . RT HAF3 175 180 = MIRA . RT SRMr 180 180 = MIRA . RT HAF5 181 224 = MIRA . RT SRMr 195 195 = MIRA . RT SRMr 199 199 = MIRA . RT HAF3 225 225 = MIRA . RT SRMr 225 225 = MIRA . RT HAF5 226 378 = MIRA . RT SRMr 228 228 = MIRA . RT SRMr 270 270 = MIRA . RT SRMr 339 339 = MIRA . RT HAF3 379 379 = MIRA . RT SRMr 379 379 = MIRA . RT HAF5 380 408 = MIRA . RT SRMr 406 406 = MIRA . RT HAF3 410 412 = MIRA . RT HAF5 413 474 = MIRA . RT SRMr 421 421 = MIRA . RT SRMr 422 422 = MIRA . RT SRMr 472 472 = MIRA . RT SRMr 475 475 = MIRA . RT HAF3 475 480 = MIRA . ER AT 365 828 17 480 // EC On 01/11/2012, at 5:00 PM, Bastien Chevreux wrote: On Nov 1, 2012, at 5:08 , Robert Trygve Good <rtgood@xxxxxxxxxxxxxx<mailto:rtgood@xxxxxxxxxxxxxx>> wrote: The MAF file is 13 mb compressed, Is there a certain part you need? Here are the head and tail of the maf. Ideally the part which contains the faulty config :-) It should start with CO end ends with the next EC CO <contigname> … … … EC where <configname> is the name you got the error. B. Rob Good rtgood@xxxxxxxxxxxxxx<mailto:rtgood@xxxxxxxxxxxxxx> Department of Genetics Royal Pde University of Melbourne 3010 +61383442347 0434058250 Rob Good rtgood@xxxxxxxxxxxxxx<mailto:rtgood@xxxxxxxxxxxxxx> Department of Genetics Royal Pde University of Melbourne 3010 +61383442347 0434058250