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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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[ERROR] svaba: STCoverage.cpp:90: void STCoverage::addRead(const SeqLib::BamRecord&, int, bool): Assertion `e - p < 1e6' failed. #77

Open angelussong opened 4 years ago

angelussong commented 4 years ago

Hi,

Sorry to bug you with this. I'm currently trying to investigate structural variance on some single-cell RNA-seq datasets I have ( a normal and tumor pair).

I started svaba on an HPC and it seemed running fine until chromosome 14 (that's the last line in the log file). However, I couldn't tell why that is. This is the output in the .error file:

--- Loaded non-read data. Starting detection pipeline svaba: STCoverage.cpp:90: void STCoverage::addRead(const SeqLib::BamRecord&, int, bool): Assertion `e - p < 1e6' failed.

And I saw two large core files in the directory.

Could you please help me identify the cause of this problem?

Thanks so much!

Hanbing Song

walaj commented 4 years ago

This is tough - for some reason svaba is detecting a read with length > 1e6 bases -- I assume this is not the case?

Although, svaba is probably not the right tool for RNA-seq datasets anyway, so hopefully you found a tool that finds what you need!