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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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ERROR! not enough genetic markers with MAF >= 0.01 #312

Closed jameskozubek closed 3 years ago

jameskozubek commented 3 years ago

M: 554270, N: 5549 size of genoVecofPointers: 1 setgeno mark1 setgeno mark2 482096 markers with MAF >= 0.01 are used for GRM. setgeno mark5 setgeno mark6 time: 37931.1 482096 markers have MAF >= 0.01 forSparseKin=200 genetic markers are randomly selected to decide which samples are related Error in createSparseGRM(plinkFile = opt$plinkFile, outputPrefix = opt$outputPrefix, : ERROR! not enough genetic markers with MAF >= 0.01 to detect which samples are related Try include at least forSparseKin=200 genetic markers with MAF >= 0.01 in the plink file Execution halted

jameskozubek commented 3 years ago

I think there was a problem with other files in the same directory that was confusing the script