[wgs-assembler-users] ContigContainment failed

[Ole K. T. <o.k...@bi...>]

Hi,
I got an assertion fail while scaffolding today. Error message:
CreateNewGraphNode()-- Contig 16085537
* Create a contig 16085537 in scaffold 131913
>>> Fixing up suspicious overlap (15370134,16085537,I) (ahg:-340 bhg:-143) to (15370134,16085537,O) (ahg:143 bhg:340) len: 137
* FOEXS: SUSPICIOUS Overlap found! Looked for
(16085537,15370134,I)[20,1044] found (15370134,16085537,O) 137
WARNING:  InsertChunkOverlap()-- Chunk overlap already exists.
NEW 15370134,16085537,O - min/max 131/142 0/0 erate 0.100000 flags
10000 overlap 137 hang 0,0 qual 0.000000 offset 0,0
OLD 15370134,16085537,O - min/max 20/1044 20/1044 erate 0.100000 flags
10001 overlap 137 hang 143,340 qual 0.000000 offset 0,0
WARNING:  CreateChunkOverlapFromEdge()-- Chunk overlap already exists.
 Keeping old overlap.
NEW 15370134,16085537,O - min/max 131/142 0/0 erate 0.100000 flags
10000 overlap 137 hang 0,0 qual 0.000000 offset 0,0
OLD 15370134,16085537,O - min/max 20/1044 20/1044 erate 0.100000 flags
10001 overlap 137 hang 143,340 qual 0.000000 offset 0,0
* Switched right-left, orientation went from I to O
* CreateAContigInScaffold() failed.
ContigContainment failed.
cgw: LeastSquaresGaps_CGW.C:1410: RecomputeOffsetsStatus
RecomputeOffsetsInScaffold(ScaffoldGraphT*, CDS_CID_t, int, int, int):
Assertion `0' failed.


This is about 30x coverage with Illumina reads; 10x combined reads
(180 bp insert, 100 nt reads and combined with FLASH), 10x PE 100 nt
reads 300 insert and 5k mate pair 100 nt reads, all error corrected
with Quake. It's probably not an optimal combination, but I'm testing
a bit and interested in the result.

Using bogart and dnc, the 5k library compared against the other two.
Other options are default.

Is that assertion something that can be fixed?

Thank you.

Ole