Re: [wgs-assembler-users] cgw error

[Walenz, B. <bw...@jc...>]

Hi, Ben-

Yes, an easy one.  I don’t know why you’re having such a difficult time.  Keep plugging away at it, I guess.

Unfortunately, you’re hitting a lot of problems that have already been fixed in the latest CA code.

b


On 6/4/13 5:27 AM, "Ben Elsworth" <el...@gm...> wrote:

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... <http://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... <http://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...>  <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_failure but keep getting the error.

Any ideas?

Cheers,

Ben