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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Error in assembly step #604

Closed senzhaocode closed 1 year ago

senzhaocode commented 2 years ago

Hello gridss developer,

Thank you for developing this tool. Now I am using it to do SV calling on WGS data (tumor - 100X and normal 50X pair). I experienced a few error reports during assemble step. For example, see attached figure.
1). Traversal of kier length ending at [X, Y] contains an invalidate subnode..... 2). Sanity check failure: found path with no support.....

These errors were reported in earlier opened issues, and I thought that they were supposed to be fixed? Could you help me sort it out. Thanks again.

Screenshot 2022-10-25 at 13 59 34 Screenshot 2022-10-25 at 13 59 17
d-cameron commented 1 year ago

These errors were reported in earlier opened issues, and I thought that they were supposed to be fixed? Could you help me sort it out. Thanks again.

These are unlikely to ever get fixed the issues don't reproduce on a subset of the data (thus making debugging extremely difficult) and the graph unload/reload work-around that is triggered fixes the immediate issue without loss.

If the reload actually triggers another fail thus a total failure of assembly (as opposed to these error messages but a successful assembly) then please send through the generated debugging file (in a subdirectory of the assembly.bam.gridss.working/ directory) as that contains the minimal subset of data for reproducing the error.