Missing and unexpected column when running chrX analysis.

[zishang30]

Dear Xiaowei

I have started running chrX analysis using generated kinship and xHemi Kinship. But when I running the command as follow : rvtest-new --inVcf ChrX.combined.reorder.vcf.gz --pheno phenotypes0602.ped --pheno-name men_INV --kinship kinship_matrix.kinship --xLabel X --xHemiKinship chrx.kinship_matrix.xHemi.kinship --meta score,cov[windowSize=500000] --dosage DS --out HRCinv_men_chr23

I found some strange message as follows: [INFO] Loaded 1386 male, 1490 female and 0 sex-unknonw samples from phenotypes.ped [INFO] Analysis begins with [ 2876 ] samples... [INFO] Family-based model specified. Loading kinship file... [INFO] DONE: Loaded kinship file [ kinship_matrix.kinship ] successfully in [ 11.0 ] seconds. [INFO] DONE: Spectral decomposition of the kinship matrix succeeded in [ 124.7 ] seconds. [INFO] Kinship eigen-decomposition file [ .xHemi.eigen ] detected and will be used for for X chromosome analysis [INFO] DONE: Loaded kinship file [ chrx.kinship_matrix.xHemi.kinship ] successfully in [ 20.9 ] seconds. [ERROR] Missing 'u1805' column! [WARN] Failed to load spectral decomposition results of the kinship matrix! [INFO] DONE: Spectral decomposition of the kinship matrix succeeded in [ 202.1 ] seconds. [INFO] Impute missing genotype to mean (by default) [INFO] Use dosage genotype from VCF flag DS. [INFO] Analysis started

It seems there are some error about missing column in kinship matrix and lead to fail to load spectral decomposition results of the kinship matrix, but after this warning message it said "Spectral decomposition of the kinship matrix succeeded". Is this Ok to run chrX analysis ? The strange thing is when I check chrx kinship matrix manually I didn't find this missing column in 'u1805'...

In addition , some times I also receive error massage about 'Unexpected column' as the previous issue...

Thank you for your help!

zishan