Re: [wgs-assembler-users] ContigContainment failed

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

On 12 June 2012 07:38, Walenz, Brian <bw...@jc...> wrote:
> Hi, Ole-
>
> After merging two scaffolds, we do a least squares estimate of the gap sizes
> in the new scaffold.  If those gap sizes imply two contigs should be merged
> (via a negative gap) we try to merge them.  This merge failed for reasons I
> haven't looked into.  Probably bad sequence alignment.
>
> I think you can safely disable this assert.  Gap size estimation might run
> through a few more iterations (with the same result) and eventually give up.
> The scaffold will have (slightly?) bogus gap sizes.  There are,
> unfortunately, plenty of other scaffolds that fail to get gap size
> estimates, so this isn't a disaster.

Great! I commented it out in the source code, and rerunning now. Thank you.

Ole

>
> b
>
>
> On 6/11/12 1:51 PM, "Ole Kristian Tørresen" <o.k...@bi...> wrote:
>
>> 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
>>
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>