elliptical confidence not calculated
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Description
Hello!
I am running smartpca with the following par file. The run goes to completion, and I get .evec and .eval files. But the confidence ellipses are not being calculated and no ellout file is generated. No errors are thrown. Am I doing something wrong with the parameter setup?
genotypename: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.geno
snpname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.snp
indivname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHCayonuWEurasiaPublishedAncSWAsia.ind
evecoutname: ellconfnoshrinkWiaHCayonuWEurasiaHO.evec
evaloutname: ellconfnoshrinkWiaHCayonuWEurasiaHO.eval
lsqproject: YES
poplistname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WestEurasiapoplistmodern.txt
outliermode: 0
numoutevec: 2
elllistname: /nobackup/kvgm94/ADNAcomm/Kelly/pop-gen/popfiltering/WiaHList.txt
elloutname: WiaHell95.out
ellconf: 0.95
Thanks,
Kelly
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Research direction
Start by reproducing the supplied smartpca run and reviewing how the elllistname, elloutname, and ellconf parameters are handled. Confirm whether the listed population file and confidence setting produce an ellout file, and document the required setup or diagnostic if they do not.
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- Tech stack
- c
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- data
- Issue type
- Bug
- Difficulty
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- Estimated time
- 1-2 days
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- Needs clarification
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