Hello @all

I working on genome wide association analysis with GenABEL, of my fungal genome data, with more than a million SNPs.

I am able to do descriptives.trait and descriptives.marker scan of my genotype and phenotype and descriptive.scan of raw data.

But when i go quality check of my data with check.marker i get bellow error

gwadata <- load.gwaa.data(phenofile="phenomean.dat",genofile="quali-fil-scaf58.raw")
ids loaded...
marker names loaded...
chromosome data loaded...
map data loaded...
allele coding data loaded...
strand data loaded...
genotype data loaded...
snp.data object created...
assignment of gwaa.data object FORCED; X-errors were not checked!
qc1 <- check.marker(gwadata)
Excluding people/markers with extremely low call rate...
1019387 markers and 29 people in total
0 people excluded because of call rate < 0.1 
958 markers excluded because of call rate < 0.1 
Passed: 1018429 markers and 29 people

RUN 1 
1018429 markers and 29 people in total
231574 (22.73835%) markers excluded as having low (<8.62069%) minor allele frequency
332801 (32.67788%) markers excluded because of low (<95%) call rate
1018429 (100%) markers excluded because they are out of HWE (FDR <0.2)

 Error in .local(x, i, j, ..., drop) : j out of range (== 0) In
 addition: Warning message: In max(j) : no non-missing arguments to
 max; returning -Inf``

Could you help me with this. I will be helpful if you please also share a script to use after quality check of the data to analyse (descriptive.marker and descriptive.scan) for further GWAS analysis

Thank you Best regards KRP