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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Core-dump possibly due to out of memory #8

Open misshie opened 8 years ago

misshie commented 8 years ago

Hi zhanxw,

Thank you for developing and maintaining RVTests.

When I use RVTests v1.9.9-29 downloaded July 29, 2016 with the '--kernel SKATO' option and a relatively large dataset insists of 1400 samples, 240,000 variants and 190,000 line set file results core-dump in a medium memory (48Gbyte) machine. Back trace information generated by gdb is attached: core_gdb.log.txt

This does not happen in a lager memory machine. Decreasing VCF file size or the '--peopleExcludeFile' option also solved the problem even in medium memory machine.

Thus, I guess this core-dump is related to out of memory stuff and I believe that it is better to return 'out of memory error'.

I am happy if my report helps RVTests development.

Best wishes, Hiro.

zhanxw commented 7 years ago

Thanks for your report. I agree with you that this problem is likely to be caused by out of memory. I will try to make rvtests to give more information in this situation.