[mira_talk] Mira v3.0.2 creased in pass four of a denovo run
- From: Christina Toft <christina.toft@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 13:41:59 +0100
Hi,
I incurred problems when running Mira v3.0.2 on a 1.6M bacterial
genome with 400K 454 Titanium + 200K (long paired-ends so 400k) Solexa
reads.
Command:
mira --project=$ASS_ID --job=denovo,genome,454,solexa,accurate
-OUT:ora=yes -GE:not=4 -AS:urd=yes:klrs=yes 454_SETTINGS
-CO:mrpg=10:mgqrt=45:mnq=30 SOLEXA_SETTINGS -LR:ft=fastq:fqqo=64 -GE
:tismin=4200:tismax=4800
Where running okay but creased in Pass four :
Hunting join spoiler
HSS At end: 1 0 HWI-EAS210R_0001:6:91:274:1361#CGATGT/2
HSS Permbans: 282
HSS remove HWI-EAS210R_0001:6:91:274:1361#CGATGT/2
HSS clip front back 1 0
HSS At end: 1 0 HWI-EAS210R_0001:6:96:1768:885#CGATGT/2
HSS Permbans: 282
HSS remove HWI-EAS210R_0001:6:96:1768:885#CGATGT/2
HSS clip front back 1 0
HSS At end: 1 0 HWI-EAS210R_0001:6:97:536:1507#CGATGT/2
HSS Permbans: 282
HSS remove HWI-EAS210R_0001:6:97:536:1507#CGATGT/2
HSS clip front back 1 0
Localtime: Sat Mar 13 11:46:50 2010
Saving debris list to file:
BBbNrIrPeM03_assembly/BBbNrIrPeM03_d_log/BBbNrIrPeM03_info_debrislist_pass.4.txt
Repeats found during contig building, adding additional alignment iteration
for quick repeat resolving.
Making alignments.
Localtime: Sat Mar 13 11:46:54 2010
Aligning possible forward matches:
[0%] ....|Len1: 429
Len2: 0
Internal logic/programming/debugging error (*sigh* this should not
have happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"len1 or len2 == 0 ?"
->Thrown: Dynamic::setSequences(const char * seq1, uint32 len1, const
char * seq2, uint32 len2, bool calcwithoffset, int32 expectedoffset)
->Caught: void Assembly::makeAlignments()
Program aborted, probably due to an internal error.
Any idea what the problem could be?
Best,
Christina
--
Christina Toft
Postdoctoral Researcher
Molecular Evolution, EBC, Uppsala University
Norbyv. 18C, 752 36 Uppsala, Sweden
Email: Christina.Toft@xxxxxxxxx
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