mya
New Member
Posts: 1
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Post by mya on Apr 27, 2020 6:57:53 GMT
Hi,
I would like to run fastGWA for haploid male non-PAR of chromosome X.
When the following way was executed, make model is success, but in association tests, the error message was output and no results were obtained...
# In association tests of female non-PAR of chromosome X, the results were obtained.
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gcta64 --mbfile List_bed_Auto.txt --grm-sparse sparse_grm --fastGWA-mlm --model-only --pheno pheno1.pheno --qcovar age.txt --covar sex.txt --keep Male.bgen.keep --threads 8 --out ChrX_Male
gcta --threads 8 --bgen ChrX.1_GP.bgen --sample ChrX.1_GP.sample --load-model ChrX_Male.fastGWA --dc 0 --pheno pheno1.pheno --qcovar age.txt --covar sex.txt --keep Male.bgen.keep --out ChrX.1_Male
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# I use gcta64 v1.93.1.
Error message:
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Error: multi ploidy detected in 3th SNP of [ChrX.1_GP.bgen].
An error occurs, please check the options or data
Error: multi ploidy detected in 0th SNP of [ChrX.1_GP.bgen].
An error occurs, please check the options or data
Error: multi ploidy detected in 5th SNP of [ChrX.1_GP.bgen].
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Is this not the right way to do it?
I would appreciate your advice.
Thank you.
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gpcr
New Member
Posts: 5
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Post by gpcr on Apr 30, 2020 17:45:50 GMT
I am getting the same error with variant ploidy? any pointers to overcome?
--bgen chrX.ALL.bgen --sample ALL.sample --load-model ALL_sp.fastGWA --threads 30 --out chrX.HRC.ALL_sp
Error: multi ploidy detected in 10th SNP of [chrX.ALL.bgen]. An error occurs, please check the options or data Error: multi ploidy detected in 1th SNP of [chrX.ALL.bgen]. Error: multi ploidy detected in 0th SNP of [chrX.ALL.bgen]. An error occurs, please check the options or data Error: multi ploidy detected in 16th SNP of [chrX.ALL.bgen]. An error occurs, please check the options or data Error: multi ploidy detected in 20th SNP of [chrX.ALL.bgen]. Error: multi ploidy detected in 19th SNP of [chrX.ALL.bgen]. An error occurs, please check the options or data Error: multi ploidy detected in 13th SNP of [chrX.ALL.bgen]. Error: multi ploidy detected in 13th SNP of [chrX.ALL.bgen].
Thank you.
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