Re: [wgs-assembler-users] cgw error

[Ben E. <el...@gm...>]

Ok, apologies, this one was easy, I just commented out the assertion on
line 1419 and all seems well again.

Cheers,

Ben

On 2 June 2013 19:59, Ben Elsworth <el...@gm...> wrote:

> Hi Brian,
>
> Thanks again for your help. I got a little further this time. Now I have
> an error again during the cgw stage but this time the error
> from 7-2-CGW/cgw.out is:
>
> * FOEXS: SUSPICIOUS Overlap found! Looked for (1184641,594183,O)[12,1073]
> found (594183,1184641,I) 20
> WARNING:  InsertChunkOverlap()-- Chunk overlap already exists.
> NEW 594183,1184641,I - min/max 17/23 0/0 erate 0.250000 flags 10000
> overlap 20 hang 0,0 qual 0 offset 0,7276224
> OLD 594183,1184641,I - min/max 12/1073 12/1073 erate 0.250000 flags 10001
> overlap 20 hang 310,300 qual 0 offset 0,7276224
> WARNING:  CreateChunkOverlapFromEdge()-- Chunk overlap already exists.
>  Keeping old overlap.
> NEW 594183,1184641,I - min/max 17/23 0/0 erate 0.250000 flags 10000
> overlap 20 hang 0,0 qual 0 offset 0,7276224
> OLD 594183,1184641,I - min/max 12/1073 12/1073 erate 0.250000 flags 10001
> overlap 20 hang 310,300 qual 0 offset 0,7276224
> * Switched right-left, orientation went from O to I
> * CreateAContigInScaffold() failed.
> ContigContainment failed.
> cgw: LeastSquaresGaps_CGW.C:1419: RecomputeOffsetsStatus
> RecomputeOffsetsInScaffold(ScaffoldGraphT*, CIScaffoldT*, int, int, int):
> Assertion `0' failed.
>
> Any ideas?
>
> Cheers,
>
> Ben
>
> On 30 May 2013 12:40, Walenz, Brian <bw...@jc...> wrote:
>
>>  Hi, Ben-
>>
>> Somehow, various flags on reads are inconsistent.  Unless you’ve got a
>> LOT of time invested in this cgw run, I’d recommend deleting the 7*
>> directories and starting scaffolding again.  Is this near the start of the
>> cgw process?  Can you get a stack trace?  If not, what does the *timing
>> file contain?  Were there any oddities in the scaffold run so far?
>>
>> It’s failing because it wants to compute the insert size of a specific
>> mate pair, but the two reads are in different contigs.  We can get around
>> the current failure by explicitly ignoring this pair.  Right before the
>> assert that fails, add:
>>
>> if (frag->contigID != mate->contigID)
>>   continue;
>>
>> I.e., Doctor, it hurts when I do this.  Then don’t do that!
>>
>> b
>>
>>
>>
>>
>> On 5/28/13 10:06 AM, "Ben Elsworth" <el...@gm...> wrote:
>>
>> Hi Brian,
>>
>> That didn't seem to help. I tried editing an earlier section of code in a
>> similar way by adding this:
>>
>> if (mateContig == NULL){
>>     continue;
>> }
>>
>> below this:
>>
>> mateContig = GetGraphNode( ScaffoldGraph->ContigGraph, mate->contigID);
>>
>> But that led to another error:
>>
>> cgw: GraphCGW_T.C:3232: void ComputeMatePairStatisticsRestricted(int,
>> int32, char*): Assertion `frag->contigID == mate->contigID' failed.
>>
>> Any idea what's going on?
>>
>> Cheers,
>>
>> Ben
>>
>> On 28 May 2013 11:00, Walenz, Brian <bw...@jc...> wrote:
>>
>> Hi Ben-
>>
>> I think this is harmless, and can be patched around.
>>
>> > To patch it up, and maybe avoid the crash here, add the following at
>> line
>> > 3206 in AS_CGW/GraphCGW_T.c
>> >
>> > if (extremeContig == NULL)
>> >   continue;
>> >
>> > Line 3206 is just after "extremeContig = GetGraphNode(...)" and before
>> the
>> > call to GetContigPositionInScaffold().
>>
>> Line numbers above are relative to the latest code base.  In 6.1, unless
>> masurca fiddled with GraphCGW_T.c, you want line 3296, in between these two
>> lines:
>>
>>           extremeContig = GetGraphNode( ScaffoldGraph->ContigGraph,
>> scaff->info.Scaffold.BEndCI);
>>           GetContigPositionInScaffold ( extremeContig, &contigLeftEnd,
>> &contigRightEnd, &contigScaffoldOrientation);
>>
>> The one other assembly that failed here (it was recent, too) finished
>> successfully after the patch.
>>
>> b
>>
>>
>>
>> On 5/27/13 7:43 AM, "Ben Elsworth" <el...@gm... <
>> http://el...@gm...> > wrote:
>>
>> Hi,
>>
>> I'm running v6.1 within MaSuRCA and keep getting this error during the
>> cgw step:
>>
>> cgw: GraphCGW_T.C:3275: void ComputeMatePairStatisticsRestricted(int,
>> int32, char*): Assertion `(mateContig) != __null' failed.
>>
>> It occurs after a lot of warnings about negative variance. I've tried
>> following the advice here -
>> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Scaffolder_failurebut keep getting the error.
>>
>> Any ideas?
>>
>> Cheers,
>>
>> Ben
>>
>>
>>
>>
>