I was hoping you could help me with an error I've been getting and haven't managed to sort out based on previous posts or feedback. I've copied my commands and the output below, but please let me know if you need any more information.
Initializing Genotype file:
/mnt/work/projects/GRS/Pure_cLBP/overlapping_SNPs/chr#_HUNT_overlapping_SNPs_only
(bed)
With external fam file: allchr_Pure_cLBP_HUNT.fam
Start processing Pure_cLBP_UKBB_results_newSNPID
Base file:
/mnt/work/projects/GWAS/Pure_cLBP_UKBB/Pure_cLBP_UKBB_results_newSNPID.txt
Header of file is:
rsID SNPID CHR POS NON_EFFECT_ALLELE EFFECT_ALLELE
AC_EFFECT_ALLELE AF_EFFECT_ALLELE BETA SE P Tstat varT
varTstar R2 MAC MAF
Reading 100.00%
62235810 variant(s) observed in base file, with:
1 variant(s) excluded as they are on unknown/sex chromosome
3010494 variant(s) located on haploid chromosome
59225315 total variant(s) included from base file
Loading Genotype info from target
Error: Cannot open file: allchr_Pure_cLBP_HUNT.fam
Hi there,
I was hoping you could help me with an error I've been getting and haven't managed to sort out based on previous posts or feedback. I've copied my commands and the output below, but please let me know if you need any more information.
Thank you in advance! -Amy
timefile=./test.time.txt /usr/bin/time -o ${timefile} -v Rscript /mnt/work/software/PRSice_v2.3.5/PRSice.R \ --prsice /mnt/work/software/PRSice_v2.3.5/PRSice_linux \ --target /mnt/work/projects/GRS/Pure_cLBP/overlapping_SNPs/chr#_HUNT_overlapping_SNPs_only,allchr_Pure_cLBP_HUNT.fam \ --keep /mnt/work/projects/GRS/unrelated.txt \ --base /mnt/work/projects/GWAS/Pure_cLBP_UKBB/Pure_cLBP_UKBB_results_newSNPID.txt \ --A1 EFFECT_ALLELE \ --stat BETA \ --pvalue P \ --snp SNPID \ --binary-target T \ --fastscore T \ --bar-levels 0.00000005,0.000001,0.0001,0.001,0.01,0.05,0.1,0.2,0.5,1 \ --score std \ --cov-file /mnt/work/projects/GRS/Pure_cLBP/HUNT_Pure_cLBP_PRS_covs_nofid.txt \ --cov-col batch,PC1,PC2,PC3,PC4 \ --clump-kb 250 \ --clump-r2 0.1 \ --clump-p 1 \ --x-range chr6:25000000-26463574,chr6:26463576-35000000 \ --ignore-fid \ --out /mnt/work/projects/GRS/Pure_cLBP/Pure_cLBP_PRS_UKBBtoHUNT
Initializing Genotype file: /mnt/work/projects/GRS/Pure_cLBP/overlapping_SNPs/chr#_HUNT_overlapping_SNPs_only (bed) With external fam file: allchr_Pure_cLBP_HUNT.fam
Start processing Pure_cLBP_UKBB_results_newSNPID
Base file: /mnt/work/projects/GWAS/Pure_cLBP_UKBB/Pure_cLBP_UKBB_results_newSNPID.txt Header of file is: rsID SNPID CHR POS NON_EFFECT_ALLELE EFFECT_ALLELE AC_EFFECT_ALLELE AF_EFFECT_ALLELE BETA SE P Tstat varT varTstar R2 MAC MAF
Reading 100.00% 62235810 variant(s) observed in base file, with: 1 variant(s) excluded as they are on unknown/sex chromosome 3010494 variant(s) located on haploid chromosome 59225315 total variant(s) included from base file
Loading Genotype info from target
Error: Cannot open file: allchr_Pure_cLBP_HUNT.fam
Error: Execution halted