Errno 2 in Association test

[dineshpeace]

I am running complete analysis using hg38, but get the following error. Your suggestion will be very useful

.... ... [9] Making reference panel for HLA-AA, SNPS,HLA, and Normal variants (SNPs) is Done!

File not foundError : Errno 2 No such file or directory : '/../../wrkingdir/.Regr.assoc.logistic'

I suppose the above file is created by the software. Can you please suggest what modification I can use

python HATK.py \ --hg 38 \ --hped example/wtccc_filtered_58C_RA.hatk.300+300.hped2 \ --bfile mydir/test1 \ --pheno mydir/test1.phe \ --pheno-name RA \ --imgt 3320 \ --imgt-dir example/IMGTHLA3320/ \ --multiprocess 8 \ --out Results/ --java-mem 4g \ --nthreads 4

Thanks for your suggestion and amazing tool.

[dineshpeace]

@WansonChoi Kindly provide your opinion on the missing file "Regr.assoc.logistic" regards Dinesh

[jaykim27]

@dineshpeace I think it has to do with your phenotype file. I also had the same problem and simply recoding phenotype as 1 & 2 not 0 & 1 fixed this issue.