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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
66 stars 9 forks source link

Segmentationfault (core dumped) in one Chromosome #97

Closed NattyandMinnie closed 4 months ago

NattyandMinnie commented 5 months ago

I have been getting a segmentation fault when running phase_common_static. I am using the latest version, and frankly, it's been working perfectly for me as I have used it a lot the last year. Now, I have this as a part of my script and it ran chromosomes 1-28 just fine, while I get this error at chromosome 29. When I look into the input file, there are variants there, they look all fine (also for sample NFH_67). I have tried with different numbers of threads (1, 2, and not specifying it). I have run it 4-5 times and I get the same error every time. So what I wonder is about the warning of no states in an sample and why the segmentation fault occurs? I attached (half) my input file to use for testing as the full size was too big for upload here.

NattyandMinnie commented 4 months ago

Ended up reinstalling the software which fixed it.