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Hi All,
I'm messing around with PSMC a bit.
I'm having trouble getting the bootstrap part to run properly. I'm sort of wondering if bwa/samtools updates are causing some issues.
The program seems to run fine for the full analysis (though I don't know if my results are reasonable or not), but I am getting division by zero errors when I try to do the bootstrap.
Seems like a lack of heterozygous sites can cause this, but that does not seem to be my issue as I have "K" sites in my psmcfa file. The problem comes in the psmc.plot step, not in the psmc run.
I know Heng Li is encouraging people to move on from PSMC, and perhaps that is reasonable, but still would like to sort this out.
Thanks!
Chris
I'm messing around with PSMC a bit.
I'm having trouble getting the bootstrap part to run properly. I'm sort of wondering if bwa/samtools updates are causing some issues.
The program seems to run fine for the full analysis (though I don't know if my results are reasonable or not), but I am getting division by zero errors when I try to do the bootstrap.
Seems like a lack of heterozygous sites can cause this, but that does not seem to be my issue as I have "K" sites in my psmcfa file. The problem comes in the psmc.plot step, not in the psmc run.
I know Heng Li is encouraging people to move on from PSMC, and perhaps that is reasonable, but still would like to sort this out.
Thanks!
Chris