Warning: no sample level data available

[michelemarongiu79]

Hi everynone,

I'm running SAIGE 0.44.2, STEP2 with step2_SPAtests.R. this is my bash file:

chr=$1 trait=$2

Rscript step2SPAtests.R \ --vcfFile=/myvcf/geno.chr$chr.vcf.gz \ --vcfFileIndex=/myvcf/geno.chr$chr.vcf.gz.tbi \ --vcfField=DS \ --chrom=$chr \ --minMAC=1 \ --GMMATmodelFile=$PWD/GRM$trait.rda \ --varianceRatioFile=$PWD/GRM$trait.varianceRatio.txt \ --SAIGEOutputFile=$PWD/GRM$trait.$chr.SAIGE.vcf.genotype.txt \ --numLinesOutput=2 \ --LOCO=TRUE

I paste the last lines with the error:

It is a quantitative trait isCondition is FALSE Analysis started at 1645531870 Seconds Warning: no sample level data available Error in if (markerInfo >= 0 & markerInfo <= 1) { : argument is of length zero Calls: SPAGMMATtest Execution halted

I think it is a mistake on the samples, can anyone help me?

Thank you all M.

[weizhouUMICH]

Hi @michelemarongiu79,

Sorry fo the late reply! We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/

The program will be maintained by multiple SAIGE developers there. Note that the csi instead of tbi index file is used for VCF input. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei