[mira_talk] Re: convert_project Error
- From: Robert Trygve Good <rtgood@xxxxxxxxxxxxxx>
- To: "<mira_talk@xxxxxxxxxxxxx>" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 2 Nov 2012 01:57:30 +0000
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
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