All association tests have failed (Association tests on 324063 groups have completed. 324063 failed)

[marionamujal]

Hello,
I am requesting for your help on this. I am running a common variant association analysis with variant tools using docker. However, all the association tests are failing. I wonder what could be the cause.
Any assistance on this will be very much appreciated!

INFO: 314 samples are found
INFO: Grouping variants by 'variant.chr:variant.pos', please be patient ...
INFO: 324063 groups are found
WARNING: Temp files are not regenerated!
Testing for association: 100% [==========================================================================] 324,063/324,025 31.7/s in 02:50:36
WARNING: Field sample_size_SNV_permute has all missing values
WARNING: No valid integer values has been found for field sample_size_SNV_permute
WARNING: Field num_variants_SNV_permute has all missing values
WARNING: No valid integer values has been found for field num_variants_SNV_permute
WARNING: Field total_mac_SNV_permute has all missing values
WARNING: No valid integer values has been found for field total_mac_SNV_permute
WARNING: Field beta_x_SNV_permute has all missing values
WARNING: No valid float values has been found for field beta_x_SNV_permute
WARNING: Field pvalue_SNV_permute has all missing values
WARNING: No valid float values has been found for field pvalue_SNV_permute
WARNING: Field std_error_SNV_permute has all missing values
WARNING: No valid float values has been found for field std_error_SNV_permute
WARNING: Field num_permutations_SNV_permute has all missing values
WARNING: No valid integer values has been found for field num_permutations_SNV_permute
**INFO: Association tests on 324063 groups have completed. 324063 failed.**
INFO: Indexing linked field variant.chr, variant.pos
INFO: Using annotation DB common_variants as common_variants in project Variant_association_tools_001.
INFO: Annotation database used to record results of association tests. Created on Thu, 05 Nov 2020 21:58:50
INFO: 324063 out of 3006180 variant.chr, variant.pos are annotated through annotation database common_variants

[BoPeng]

Could you at least send the exact command that you have used? There could be many reasons and it is difficult for me to diagnose without a test project.

[Karthick99-S]

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##fileformat=VCFv4.1
##fileDate=20130319
##source=GenerateReportDataAndVCFv2.2.2.0
##reference=HumanNCBI37_UCSC
##phasing=none
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=TI,Number=.,Type=String,Description="Transcript ID">
##INFO=<ID=GI,Number=.,Type=String,Description="Gene ID">
##INFO=<ID=EXON,Number=0,Type=Flag,Description="Exon Region">
##INFO=<ID=FC,Number=.,Type=String,Description="Functional Consequence">
##FILTER=<ID=q20,Description="Quality below 20">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	12AD50320_MAXGT	12AD50320_POLY
chr16	60054	rs62028702	A	C	23	PASS	DP=9	GT:GQ	0/1:23	0/1:56
chr16	60087	rs62028703	C	G	27	PASS	DP=13	GT:GQ	0/1:27	0/1:60
chr16	60095	rs62028704	G	T	26	PASS	DP=13	GT:GQ	0/1:26	0/1:59
chr16	60120	.	G	A	11	q20	DP=10	GT:GQ	1/0:11	1/0:43

this is my vcf file i don't understand MAXGT and POLY. how to remove MAXGT AND POLY, i am go to gwas study but thia MAXGT AND POLY was my problem . pls any one help me