samreenzafer
commented
3 years ago Did you ever figure out the problem to this? I'm getting the same issue. I'm calculating the genetic correlation of our trait against some of the published UKBB_LDSC sumstats provided by NealeLab at https://nealelab.github.io/UKBB_ldsc/downloads.html#ldsc_sumstat_files Not all of them give this error though.
Steven-Shixq
igumnov-daniel
I wanted to estimate genetic correlation between two binary trait, The summary statistics beta and se are based logistic regression. Their Zscores range are [-8.881,7.614], and [-4.398,5.029]. When I used the following command line, the rg will produce the errors. Can you give me some advice on how to fix them? Thanks! Best regards! Hanson
Call: ./ldsc.py \ --ref-ld-chr eur_w_ld_chr/ \ --out ./pgc3_genderAge_BiploarStatus_regenie \ --rg ./daner_bip_pgc3_nm_Subcolumn.w_hm3.sumstats.gz,./test_bin_out_firth_EUR_2var_BT_Status_Bipolar.regenie_subcol.w_hm3.sumstats.gz \ --w-ld-chr eur_w_ld_chr/
Beginning analysis at Mon Sep 28 16:17:44 2020 Reading summary statistics from ./daner_bip_pgc3_nm_Subcolumn.w_hm3.sumstats.gz ... Read summary statistics for 1090822 SNPs. Reading reference panel LD Score from eur_w_ld_chr/[1-22] ... Read reference panel LD Scores for 1290028 SNPs. Removing partitioned LD Scores with zero variance. Reading regression weight LD Score from eur_w_ld_chr/[1-22] ... Read regression weight LD Scores for 1290028 SNPs. After merging with reference panel LD, 1086428 SNPs remain. After merging with regression SNP LD, 1086428 SNPs remain. Computing rg for phenotype 2/2 Reading summary statistics from ./test_bin_out_firth_EUR_2var_BT_Status_Bipolar.regenie_subcol.w_hm3.sumstats.gz ... Read summary statistics for 1217311 SNPs. After merging with summary statistics, 1086428 SNPs remain. 786449 SNPs with valid alleles. ERROR computing rg for phenotype 2/2, from file /home/hanl3/cmc/BioVU_Mega/scratch/GWAS_Analysis/test_bin_out_firth_EUR_2var_BT_Status_Bipolar.regenie_subcol.w_hm3.sumstats.gz. Traceback (most recent call last): File "/gpfs52/data/ruderferlab/software/ldsc/ldscore/sumstats.py", line 410, in estimate_rg rghat = _rg(loop, args, log, M_annot, ref_ld_cnames, w_ld_cname, i) File "/gpfs52/data/ruderferlab/software/ldsc/ldscore/sumstats.py", line 537, in _rg intercept_gencov=intercepts[2], n_blocks=n_blocks, twostep=args.two_step) File "/gpfs52/data/ruderferlab/software/ldsc/ldscore/regressions.py", line 705, in init np.multiply(hsq1.tot_delete_values, hsq2.tot_delete_values)) FloatingPointError: invalid value encountered in sqrt
Summary of Genetic Correlation Results p1 p2 rg se z p h2_obs h2_obs_se h2_int h2_int_se gcov_int gcov_int_se /home/hanl3/cmc/BioVU_Mega/scratch/GWAS_Analysis/daner_bip_pgc3_nm_Subcolumn.w_hm3.sumstats.gz /home/hanl3/cmc/BioVU_Mega/scratch/GWAS_Analysis/test_bin_out_firth_EUR_2var_BT_Status_Bipolar.regenie_subcol.w_hm3.sumstats.gz NA NA NA NA NA NA NA NA NA NA
Analysis finished at Mon Sep 28 16:17:57 2020 Total time elapsed: 13.18s