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#174 7-0-CGW failed
Hi,
I am running RUNCA to assemble a genome with only solexa reads. I encountered many errors during 5-consensus step but I corrected them. After finishing 5-consensus step, I faced cgw failed in 7-0-CGW step. The error information is below:
Splitting unitig 59656730 into as many as 3 unitigs at intervals: 301,304
Splitting unitig 59687736 into as many as 3 unitigs at intervals: 1710,1722
Splitting unitig 59687873 into as many as 3 unitigs at intervals: 281,284
* BuildGraphEdgesDirectly
* Frag 62076102 with iid 62076102 of cid 59497015 has ci = 59687886!!!
cgw: GraphCGW_T.C:2104: void BuildGraphEdgesFromMultiAlign(GraphCGW_T*, NodeCGW_T*, MultiAlignT*, GraphEdgeStatT*, int): Assertion `frag->cid == node->id' failed.
Does it mean that frag 62076102 exists in both unitig 59497015 and 59687886? How to correct it?
Thank you very much!
Patch for Input_CGW.c to check unitigs & fragments as they are loaded.
I'm hoping that you are correct - that the fragment is in two unitigs.
The attached patch will make cgw check for duplicate fragments when it is loading unitigs. Apply it with "cd src/AS_CGW ; patch < Input_CGW.c.patch" and recompile.
If this is the case, I'd suspect one of your fixes to 5-consensus added the same fragment to two different unitigs. The only way I can think to determine this is to dump ALL unitig layouts from tigStore version 2 and check for the presence of this fragment:
tigStore -g *gkpStore -t *tigStore 2 -d layout -U | grep 62076102
You could try looking at just those two unitigs, but I don't know if the IDs reported by CGW are the same IDs used by tigStore.
I am marking this case Pending so it will close automatically unless we hear back from the user.