search

Yves-CHEN / DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.
GNU Lesser General Public License v3.0
21 stars 6 forks source link

Error and warning message #16

Open priyambial123 opened 1 year ago

priyambial123 commented 1 year ago

Hello

I ran the dentist with GWAS summary statistics data. It stopped with an error that a SNP with maf of 0 found. Should maf which are 0 be removed in the input file.

There was also a warning that mogan is likely to be missing. What does it mean. Please find the below run with warning and error messages

Thanks

--gwas-summary /scicore/home/cichon/thirun0000/vegas_ch/dentist/dentistGCTA_pgc3.txt
--bfile /scicore/home/cichon/thirun0000/vegas_ch/g1000p3_EUR/g1000p3_EUR
--out results.txt
Reading GWAS summary data from [/scicore/home/cichon/thirun0000/vegas_ch/dentist/dentistGCTA_pgc3.txt].
Reserving 1 M memory for reading.
GWAS summary data of 7608184 SNPs to be included from [/scicore/home/cichon/thirun0000/vegas_ch/dentist/dentistGCTA_pgc3.txt].
[warning] mogan is like to be missing, but it will only be a problem when calling for it.
[info] Calculating frequencies with 1 cpus
[info] This bed file is plink 1.0 bedfile format. (Older)
[error]  A SNP(s) with maf of 0 is found.
Ruwanmali commented 10 months ago

Hello, I also have the same issue. Have you resolved this issue?