single variant test runs but group test on the same input files reports "The chunk is empty"

[cteerlink101]

Hi,

I am using this command to run SINGLE VARIANT tests (this runs successfully):

saige step2_SPAtests.R --vcf=./A2M.rehead.vcf.gz --vcfField=GT --GMMATmodelFile=afr.rda --varianceRatioFile=./afr.varianceRatio.txt --SAIGEOutputFile=./A2M.out.txt --is_Firth_beta=TRUE --pCutoffforFirth=0.05 --LOCO=FALSE --is_output_moreDetails=TRUE --chrom=12 --dosage_zerod_cutoff=0 --dosage_zerod_MAC_cutoff=0 --minMAC=1 --minMAF=0.000001

When I use this command on the same input files to run GROUP tests, it produces "The chunk is empty":

saige step2_SPAtests.R --vcf=./A2M.rehead.vcf.gz --vcfField=GT --GMMATmodelFile=afr.rda --varianceRatioFile=./afr.varianceRatio.txt --SAIGEOutputFile=./A2M.out.txt --is_Firth_beta=TRUE --pCutoffforFirth=0.05 --LOCO=FALSE --is_output_moreDetails=TRUE --chrom=12 --dosage_zerod_cutoff=0 --dosage_zerod_MAC_cutoff=0 --minMAC=1 --minMAF=0.000001 --groupFile=./A2M.grp

where A2M.grp has the format:
A2M var chr12:9069789:G:A chr12:9074600:G:A [etc...]
A2M anno lof lof [etc...]

and A2M.rehead.vcf.gz has the format:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IDs [etc]
12 9069789 chr12:9069789:G:A G A . . . GT 0/0 [etc]
12 9074600 chr12:9074600:G:A G A . . . GT 0/0 [etc]

I have tried all kinds of things but I cannot get the second command to produce any output. Can you see what might be wrong?

Thanks!

[cteerlink101]

I figured this out. I had to change the names of the snps in the vcf and the group file to not contain the string 'chr', then it ran.