LDSC in gwaslab

Example

import gwaslab as gl

Example

gl.show_version()

stdout:

2025/12/26 11:46:12 GWASLab v4.0.0 https://cloufield.github.io/gwaslab/
2025/12/26 11:46:12 (C) 2022-2025, Yunye He, Kamatani Lab, GPL-3.0 license, gwaslab@gmail.com
2025/12/26 11:46:12 Python version: 3.12.0 | packaged by conda-forge | (main, Oct  3 2023, 08:43:22) [GCC 12.3.0]

Loading and filter in only Hapmap3 SNPs

Example

t2d = gl.Sumstats("../0_sample_data/t2d_bbj.txt.gz",
             snpid="SNP",
             chrom="CHR",
             pos="POS",
             ea="ALT",
             nea="REF",
             beta="BETA",
             se="SE",
             p="P",
             direction="Dir",
             build="19",             
             n="N", verbose=False)
t2d.basic_check(verbose=False)

SNPID	CHR	POS	EA	NEA	STATUS	BETA	SE	P	DIRECTION	N
1:725932_G_A	1	725932	G	A	1960099	-0.0737	0.1394	0.5970	-?+-	166718
1:725933_A_G	1	725933	G	A	1960099	0.0737	0.1394	0.5973	+?-+	166718
1:737801_T_C	1	737801	C	T	1960099	0.0490	0.1231	0.6908	+?-+	166718
1:749963_T_TAA	1	749963	TAA	T	1960399	0.0213	0.0199	0.2846	-?++	166718
1:751343_T_A	1	751343	T	A	1960099	0.0172	0.0156	0.2705	-?++	166718
...	...	...	...	...	...	...	...	...	...	...
X:154874837_A_G	23	154874837	G	A	1960099	-0.0064	0.0117	0.5840	-+-+	191764
X:154875192_GTACTC_G	23	154875192	GTACTC	G	1960399	0.0071	0.0122	0.5612	+-+-	191764
X:154879115_A_G	23	154879115	G	A	1960099	-0.0070	0.0122	0.5646	-+-+	191764
X:154880669_T_A	23	154880669	T	A	1960099	0.0071	0.0122	0.5618	+-+-	191764
X:154880917_C_T	23	154880917	C	T	1960099	0.0072	0.0122	0.5570	+-+-	191764

Example

t2d.filter_hapmap3(inplace=True)

stdout:

2025/12/26 11:47:07  -Genomic coordinates are based on GRCh37/hg19...
2025/12/26 11:47:07 Start to extract HapMap3 SNPs ...(v4.0.0)
2025/12/26 11:47:07  -Loading Hapmap3 variants from built-in datasets...
2025/12/26 11:47:08  -Since rsID not in sumstats, CHR:POS( build 19) will be used for matching...
2025/12/26 11:47:10  -Checking if alleles are same...
2025/12/26 11:47:10  -Variants with matched alleles: 1092430
2025/12/26 11:47:10  -Raw input contains 1092430 Hapmap3 variants based on CHR:POS...
2025/12/26 11:47:10 Finished extracting HapMap3 SNPs.

Heritability estimation

Example

# available since v3.4.39
t2d.estimate_h2_by_ldsc(ref_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_ldscores/", 
                         w_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_ldscores/")

stdout:

2025/12/26 11:47:11  -Genomic coordinates are based on GRCh37/hg19...
2025/12/26 11:47:11 Start to extract HapMap3 SNPs ...(v4.0.0)
2025/12/26 11:47:11  -Current Dataframe shape : 1092430 x 12 ; Memory usage: 105.20 MB
2025/12/26 11:47:11  -Loading Hapmap3 variants from built-in datasets...
2025/12/26 11:47:11  -rsID will be used for matching...
2025/12/26 11:47:12  -Raw input contains 1213752 Hapmap3 variants based on rsID...
2025/12/26 11:47:12  -Checking if alleles are same...
2025/12/26 11:47:13  -Filtered 0 Hapmap3 variants due to unmatched alleles...
2025/12/26 11:47:13 Finished extracting HapMap3 SNPs.
2025/12/26 11:47:13 Start to run LD score regression ...(v4.0.0)
2025/12/26 11:47:13  -Current Dataframe shape : 1213752 x 13 ; Memory usage: 125.56 MB
2025/12/26 11:47:13  -Run single variate LD score regression:
2025/12/26 11:47:13   -Adopted from LDSC source code: https://github.com/bulik/ldsc
2025/12/26 11:47:13   -Please cite LDSC: Bulik-Sullivan, et al. LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies. Nature Genetics, 2015.
2025/12/26 11:47:13  -Arguments:
2025/12/26 11:47:13   -ref_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_ldscores/
2025/12/26 11:47:13   -w_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_ldscores/
2025/12/26 11:47:14  -LDSC log:
2025/12/26 11:47:14   -Reading reference panel LD Score from /home/yunye/tools/ldsc/ldscores/eas_ldscores/[1-22] ... (ldscore_fromlist)
2025/12/26 11:47:15   -Read reference panel LD Scores for 1208050 SNPs.
2025/12/26 11:47:15   -Removing partitioned LD Scores with zero variance.
2025/12/26 11:47:15   -Reading regression weight LD Score from /home/yunye/tools/ldsc/ldscores/eas_ldscores/[1-22] ... (ldscore_fromlist)
2025/12/26 11:47:16   -Read regression weight LD Scores for 1208050 SNPs.
2025/12/26 11:47:16   -After merging with reference panel LD, 1079390 SNPs remain.
2025/12/26 11:47:17   -After merging with regression SNP LD, 1079390 SNPs remain.
2025/12/26 11:47:17   -Using two-step estimator with cutoff at 30.
2025/12/26 11:47:17  -Results have been stored in .ldsc_h2
2025/12/26 11:47:17  -Current Dataframe shape : 1213752 x 14 ; Memory usage: 134.82 MB
2025/12/26 11:47:17 Finished running LD score regression.

Example

t2d.ldsc_h2

h2_obs	h2_se	Lambda_gc	Mean_chi2	Intercept	Intercept_se	Ratio	Ratio_se	Catagories
0.10394433	0.00650644	1.32982693	1.49125406	1.09147712	0.01056279	0.18621142	0.02150169	NA

Genetic correlation

Example

bmi_female = gl.Sumstats("../0_sample_data/bbj_bmi_female.txt.gz",fmt="auto",ea="REF",nea="ALT",rsid="SNP",n=70000, sep="\t",build="19",verbose=False)
bmi_male = gl.Sumstats("../0_sample_data/bbj_bmi_male.txt.gz",fmt="auto",ea="REF",nea="ALT",rsid="SNP",n=80000,sep="\t",build="19",verbose=False)

other_traits : a list of gl.Sumstats object
rg : alias for each trait including the main trait

Example

# available since v3.4.39
t2d.estimate_rg_by_ldsc(other_traits=[bmi_female,bmi_male], 
                               rg="T2D,BMI_female,BMI_male",
                               ref_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_ldscores/", 
                               w_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_ldscores/")

stdout:

2025/12/26 11:47:32  -Genomic coordinates are based on GRCh37/hg19...
2025/12/26 11:47:32 Start to extract HapMap3 SNPs ...(v4.0.0)
2025/12/26 11:47:32  -Current Dataframe shape : 1092430 x 12 ; Memory usage: 105.20 MB
2025/12/26 11:47:32  -Loading Hapmap3 variants from built-in datasets...
2025/12/26 11:47:33  -rsID will be used for matching...
2025/12/26 11:47:34  -Raw input contains 1213752 Hapmap3 variants based on rsID...
2025/12/26 11:47:34  -Checking if alleles are same...
2025/12/26 11:47:35  -Filtered 0 Hapmap3 variants due to unmatched alleles...
2025/12/26 11:47:35 Finished extracting HapMap3 SNPs.
2025/12/26 11:47:35 Start to run LD score regression for genetic correlation ...(v4.0.0)
2025/12/26 11:47:35  -Current Dataframe shape : 1213752 x 13 ; Memory usage: 125.56 MB
2025/12/26 11:47:35  -Run cross-trait LD score regression:
2025/12/26 11:47:35   -Adopted from LDSC source code: https://github.com/bulik/ldsc
2025/12/26 11:47:35   -Please cite LDSC: Bulik-Sullivan, B., et al. An Atlas of Genetic Correlations across Human Diseases and Traits. Nature Genetics, 2015.
2025/12/26 11:47:35  -Arguments:
2025/12/26 11:47:35   -rg:T2D,BMI_female,BMI_male
2025/12/26 11:47:35   -ref_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_ldscores/
2025/12/26 11:47:35   -w_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_ldscores/
2025/12/26 11:47:35  -Processing sumstats with alias BMI_female (Study_1)
2025/12/26 11:47:36  -Processing sumstats with alias BMI_male (Study_1)
2025/12/26 11:47:36  -LDSC log:
2025/12/26 11:47:36   -Reading reference panel LD Score from /home/yunye/tools/ldsc/ldscores/eas_ldscores/[1-22] ... (ldscore_fromlist)
2025/12/26 11:47:37   -Read reference panel LD Scores for 1208050 SNPs.
2025/12/26 11:47:37   -Removing partitioned LD Scores with zero variance.
2025/12/26 11:47:37   -Reading regression weight LD Score from /home/yunye/tools/ldsc/ldscores/eas_ldscores/[1-22] ... (ldscore_fromlist)
2025/12/26 11:47:38   -Read regression weight LD Scores for 1208050 SNPs.
2025/12/26 11:47:39   -After merging with reference panel LD, 1079390 SNPs remain.
2025/12/26 11:47:39   -After merging with regression SNP LD, 1079390 SNPs remain.
2025/12/26 11:47:39   -Computing rg for phenotype 2/3
2025/12/26 11:47:40   -Read summary statistics for 5961600 SNPs.
2025/12/26 11:47:44   -After merging with summary statistics, 1021957 SNPs remain.
2025/12/26 11:47:45   -1021957 SNPs with valid alleles.
2025/12/26 11:47:45   -Heritability of phenotype 1
2025/12/26 11:47:45   -Total Observed scale h2: 0.09687973 (0.00885768)
                       -Lambda GC: 1.34889231
                       -Mean Chi^2: 1.50928684
                       -Intercept: 1.12024032 (0.02516315)
                       -Ratio: 0.23609547 (0.04940861)
2025/12/26 11:47:45   -Heritability of phenotype 2/3
2025/12/26 11:47:45   -Total Observed scale h2: 0.19319917 (0.01213263)
                       -Lambda GC: 1.2537503
                       -Mean Chi^2: 1.31732059
                       -Intercept: 1.0306093 (0.01022627)
                       -Ratio: 0.09646175 (0.03222695)
2025/12/26 11:47:45   -Genetic Covariance
2025/12/26 11:47:45   -Total Observed scale gencov: 0.04387074 (0.00729069)
                       -Mean z1*z2: 0.12628027
                       -Intercept: 0.01918354 (0.00945413)
2025/12/26 11:47:45   -Genetic Correlation
2025/12/26 11:47:45   -Genetic Correlation: 0.32066816 (0.06227918)
                       -Z-score: 5.14888223
                       -P: 2.62043342e-07

2025/12/26 11:47:45   -Computing rg for phenotype 3/3
2025/12/26 11:47:46   -Read summary statistics for 5961600 SNPs.
2025/12/26 11:47:50   -After merging with summary statistics, 1021957 SNPs remain.
2025/12/26 11:47:51   -1021957 SNPs with valid alleles.
2025/12/26 11:47:51   -Heritability of phenotype 3/3
2025/12/26 11:47:51   -Total Observed scale h2: 0.17595184 (0.01138382)
                       -Lambda GC: 1.25741577
                       -Mean Chi^2: 1.34453038
                       -Intercept: 1.04768706 (0.01071735)
                       -Ratio: 0.13841176 (0.03110712)
2025/12/26 11:47:51   -Genetic Covariance
2025/12/26 11:47:51   -Total Observed scale gencov: 0.02739806 (0.00705736)
                       -Mean z1*z2: 0.07617508
                       -Intercept: 0.00535343 (0.0118926)
2025/12/26 11:47:51   -Genetic Correlation
2025/12/26 11:47:51   -Genetic Correlation: 0.20984874 (0.06008801)
                       -Z-score: 3.49235659
                       -P: 0.00047878

2025/12/26 11:47:51 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
T2D BMI_female 0.320668 0.062279 5.148882 2.620433e-07 0.193199   0.012133 1.030609   0.010226  0.019184     0.009454
T2D   BMI_male 0.209849 0.060088 3.492357 4.787786e-04 0.175952   0.011384 1.047687   0.010717  0.005353     0.011893

2025/12/26 11:47:51  -Results have been stored in .ldsc_rg
2025/12/26 11:47:51 Finished running LD score regression for genetic correlation.

p1	p2	rg	se	z	p	h2_obs	h2_obs_se	h2_int	h2_int_se	gcov_int	gcov_int_se
T2D	BMI_female	0.320668	0.062279	5.148882	2.620433e-07	0.193199	0.012133	1.030609	0.010226	0.019184	0.009454
T2D	BMI_male	0.209849	0.060088	3.492357	4.787786e-04	0.175952	0.011384	1.047687	0.010717	0.005353	0.011893

Example

t2d.ldsc_rg

p1	p2	rg	se	z	p	h2_obs	h2_obs_se	h2_int	h2_int_se	gcov_int	gcov_int_se
T2D	BMI_female	0.320668	0.062279	5.148882	2.620433e-07	0.193199	0.012133	1.030609	0.010226	0.019184	0.009454
T2D	BMI_male	0.209849	0.060088	3.492357	4.787786e-04	0.175952	0.011384	1.047687	0.010717	0.005353	0.011893

visualization using plot_rg

Example

fig, ax, log, df = gl.plot_rg(t2d.ldsc_rg)

stdout:

2025/12/26 11:47:51 Start to create ldsc genetic correlation heatmap...
2025/12/26 11:47:51 Configured plot style for plot_rg:None
2025/12/26 11:47:51 Raw dataset records: 2
2025/12/26 11:47:51  -Raw dataset non-NA records: 2
2025/12/26 11:47:51 Filling diagonal line and duplicated pair for plotting...
2025/12/26 11:47:51 Valid unique trait pairs: 2
2025/12/26 11:47:51  -Valid unique trait1: 1
2025/12/26 11:47:51  -Valid unique trait2: 2
2025/12/26 11:47:51  -Significant correlations with P < 0.05: 2
2025/12/26 11:47:51  -Significant correlations after Bonferroni correction: 2
2025/12/26 11:47:51  -Significant correlations with FDR <0.05: 2
2025/12/26 11:47:51 Plotting heatmap...
2025/12/26 11:47:51 Full cell : fdr-corrected P == 0.05
2025/12/26 11:47:51 P value annotation text (Order: Bon -> FDR -> Pnom): 
2025/12/26 11:47:51  -* : non-corrected P < 0.05 
2025/12/26 11:47:51  -** : fdr-corrected P < 0.05 
2025/12/26 11:47:51  -*** : bon-corrected P < 0.05 
2025/12/26 11:47:51 Finished creating ldsc genetic correlation heatmap!

Output image

Partitioned h2

Example

# available since v3.4.40
t2d.estimate_partitioned_h2_by_ldsc(       ref_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_baseline/baselineLD2_2/baselineLD.", 
                               w_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_weights/weights.EAS.hm3_noMHC.",
                               frqfile_chr= "/home/yunye/tools/ldsc/ldscores/eas_frq/1000G.EAS.QC.",
                               overlap_annot = True, 
                               print_coefficients = True, 
                               print_delete_vals=True)

stdout:

2025/12/26 11:47:51  -Genomic coordinates are based on GRCh37/hg19...
2025/12/26 11:47:51 Start to extract HapMap3 SNPs ...(v4.0.0)
2025/12/26 11:47:51  -Current Dataframe shape : 1092430 x 12 ; Memory usage: 105.20 MB
2025/12/26 11:47:51  -Loading Hapmap3 variants from built-in datasets...
2025/12/26 11:47:52  -rsID will be used for matching...
2025/12/26 11:47:53  -Raw input contains 1213752 Hapmap3 variants based on rsID...
2025/12/26 11:47:53  -Checking if alleles are same...
2025/12/26 11:47:54  -Filtered 0 Hapmap3 variants due to unmatched alleles...
2025/12/26 11:47:54 Finished extracting HapMap3 SNPs.
2025/12/26 11:47:54 Start to run LD score regression ...(v4.0.0)
2025/12/26 11:47:54  -Run partitioned LD score regression:
2025/12/26 11:47:54   -Adopted from LDSC source code: https://github.com/bulik/ldsc
2025/12/26 11:47:54   -Please cite LDSC: Bulik-Sullivan, et al. LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies. Nature Genetics, 2015.
2025/12/26 11:47:54  -Arguments:
2025/12/26 11:47:54   -ref_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_baseline/baselineLD2_2/baselineLD.
2025/12/26 11:47:54   -w_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_weights/weights.EAS.hm3_noMHC.
2025/12/26 11:47:54   -frqfile_chr:/home/yunye/tools/ldsc/ldscores/eas_frq/1000G.EAS.QC.
2025/12/26 11:47:54   -overlap_annot:True
2025/12/26 11:47:54   -print_coefficients:True
2025/12/26 11:47:54   -print_delete_vals:True
2025/12/26 11:47:54  -LDSC log:
2025/12/26 11:47:55   -Reading reference panel LD Score from /home/yunye/tools/ldsc/ldscores/eas_baseline/baselineLD2_2/baselineLD.[1-22] ... (ldscore_fromlist)
2025/12/26 11:48:05   -Read reference panel LD Scores for 1071448 SNPs.
2025/12/26 11:48:05   -Removing partitioned LD Scores with zero variance.
2025/12/26 11:48:05   -Reading regression weight LD Score from /home/yunye/tools/ldsc/ldscores/eas_weights/weights.EAS.hm3_noMHC.[1-22] ... (ldscore_fromlist)
2025/12/26 11:48:06   -Read regression weight LD Scores for 1071448 SNPs.
2025/12/26 11:48:07   -After merging with reference panel LD, 1061153 SNPs remain.
2025/12/26 11:48:09   -After merging with regression SNP LD, 1061153 SNPs remain.
2025/12/26 11:48:09   -Removed 49 SNPs with chi^2 > 191.764 (1061104 SNPs remain)
2025/12/26 11:48:11   -Printing block jackknife delete values to ldsc.delete.
2025/12/26 11:48:11   -Printing partitioned block jackknife delete values to ldsc.part_delete.
2025/12/26 11:48:11   -Reading annot matrix from /home/yunye/tools/ldsc/ldscores/eas_baseline/baselineLD2_2/baselineLD.[1-22] ... (annot)
2025/12/26 11:49:05  -Results have been stored in .ldsc_h2
2025/12/26 11:49:05 Finished running LD score regression.

Category	Prop._SNPs	Prop._h2	Prop._h2_std_error	Enrichment	Enrichment_std_error	Enrichment_p	Coefficient	Coefficient_std_error	Coefficient_z-score
baseL2_0	1.000000	1.000000	0.000000	1.000000	0.000000	NA	-1.927388e-08	1.156327e-08	-1.666820
Coding_UCSC.bedL2_0	0.014196	0.068254	0.034691	4.808050	2.443726	0.118872	-2.544919e-08	9.348275e-08	-0.272234
Coding_UCSC.bed.flanking.500L2_0	0.049260	0.072198	0.047989	1.465653	0.974189	0.631156	-9.865231e-09	2.466959e-08	-0.399894
Conserved_LindbladToh.bedL2_0	0.024551	0.088877	0.057129	3.620093	2.326953	0.250205	2.010761e-08	9.386840e-08	0.214211
Conserved_LindbladToh.bed.flanking.500L2_0	0.305295	0.649833	0.100456	2.128542	0.329046	0.001299	-5.694877e-09	1.189500e-08	-0.478762
...	...	...	...	...	...	...	...	...	...
Ancient_Sequence_Age_Human_EnhancerL2_0	0.005145	0.078218	0.024054	15.202940	4.675287	0.002975	3.149492e-07	1.103395e-07	2.854366
Ancient_Sequence_Age_Human_Enhancer.flanking.5...	0.009070	0.011566	0.026086	1.275182	2.876194	0.923485	5.790740e-09	6.996917e-08	0.082761
Human_Enhancer_Villar_Species_Enhancer_CountL2_0	0.066854	0.212233	0.072376	3.174600	1.082602	0.04309	4.797773e-09	5.983189e-09	0.801875
Human_Promoter_Villar_ExACL2_0	0.002439	0.056685	0.041189	23.242748	16.889064	0.187759	2.645270e-07	3.249973e-07	0.813936
Human_Promoter_Villar_ExAC.flanking.500L2_0	0.000567	-0.009555	0.017212	-16.857889	30.365859	0.556254	-1.734589e-08	6.804492e-07	-0.025492

[97 rows x 10 columns]

Example

t2d.ldsc_partitioned_h2_summary

h2_obs	h2_se	Lambda_gc	Mean_chi2	Intercept	Intercept_se	Ratio	Ratio_se
0.11773265	0.00727336	1.33210306	1.47668034	1.07649298	0.01228635	0.16047018	0.02577482

Example

t2d.ldsc_partitioned_h2_results

Category	Prop._SNPs	Prop._h2	Prop._h2_std_error	Enrichment	Enrichment_std_error	Enrichment_p	Coefficient	Coefficient_std_error	Coefficient_z-score
baseL2_0	1.000000	1.000000	0.000000	1.000000	0.000000	NA	-1.927388e-08	1.156327e-08	-1.666820
Coding_UCSC.bedL2_0	0.014196	0.068254	0.034691	4.808050	2.443726	0.118872	-2.544919e-08	9.348275e-08	-0.272234
Coding_UCSC.bed.flanking.500L2_0	0.049260	0.072198	0.047989	1.465653	0.974189	0.631156	-9.865231e-09	2.466959e-08	-0.399894
Conserved_LindbladToh.bedL2_0	0.024551	0.088877	0.057129	3.620093	2.326953	0.250205	2.010761e-08	9.386840e-08	0.214211
Conserved_LindbladToh.bed.flanking.500L2_0	0.305295	0.649833	0.100456	2.128542	0.329046	0.001299	-5.694877e-09	1.189500e-08	-0.478762
...	...	...	...	...	...	...	...	...	...
Ancient_Sequence_Age_Human_EnhancerL2_0	0.005145	0.078218	0.024054	15.202940	4.675287	0.002975	3.149492e-07	1.103395e-07	2.854366
Ancient_Sequence_Age_Human_Enhancer.flanking.5...	0.009070	0.011566	0.026086	1.275182	2.876194	0.923485	5.790740e-09	6.996917e-08	0.082761
Human_Enhancer_Villar_Species_Enhancer_CountL2_0	0.066854	0.212233	0.072376	3.174600	1.082602	0.04309	4.797773e-09	5.983189e-09	0.801875
Human_Promoter_Villar_ExACL2_0	0.002439	0.056685	0.041189	23.242748	16.889064	0.187759	2.645270e-07	3.249973e-07	0.813936
Human_Promoter_Villar_ExAC.flanking.500L2_0	0.000567	-0.009555	0.017212	-16.857889	30.365859	0.556254	-1.734589e-08	6.804492e-07	-0.025492

[97 rows x 10 columns]

Cell type specific

Example

# available since v3.4.40
t2d.estimate_h2_cts_by_ldsc(ref_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_baseline/baseline1_2/baseline.", 
                            ref_ld_chr_cts = "/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Multi_tissue_gene_expr.EAS.ldcts.new",
                            w_ld_chr = "/home/yunye/tools/ldsc/ldscores/eas_weights/weights.EAS.hm3_noMHC.")

stdout:

2025/12/26 11:52:41  -Genomic coordinates are based on GRCh37/hg19...
2025/12/26 11:52:41 Start to extract HapMap3 SNPs ...(v4.0.0)
2025/12/26 11:52:41  -Current Dataframe shape : 1092430 x 12 ; Memory usage: 105.20 MB
2025/12/26 11:52:41  -Loading Hapmap3 variants from built-in datasets...
2025/12/26 11:52:41  -rsID will be used for matching...
2025/12/26 11:52:42  -Raw input contains 1213752 Hapmap3 variants based on rsID...
2025/12/26 11:52:42  -Checking if alleles are same...
2025/12/26 11:52:43  -Filtered 0 Hapmap3 variants due to unmatched alleles...
2025/12/26 11:52:43 Finished extracting HapMap3 SNPs.
2025/12/26 11:52:43 Start to run LD score regression ...(v4.0.0)
2025/12/26 11:52:44  -Run cell type specific LD score regression:
2025/12/26 11:52:44   -Adopted from LDSC source code: https://github.com/bulik/ldsc
2025/12/26 11:52:44   -Please cite LDSC: Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., ... & Price, A. L. (2018). Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature genetics, 50(4), 621-629.
2025/12/26 11:52:44  -Arguments:
2025/12/26 11:52:44   -ref_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_baseline/baseline1_2/baseline.
2025/12/26 11:52:44   -ref_ld_chr_cts:/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Multi_tissue_gene_expr.EAS.ldcts.new
2025/12/26 11:52:44   -w_ld_chr:/home/yunye/tools/ldsc/ldscores/eas_weights/weights.EAS.hm3_noMHC.
2025/12/26 11:52:44  -LDSC log:
2025/12/26 11:52:44   -Reading reference panel LD Score from /home/yunye/tools/ldsc/ldscores/eas_baseline/baseline1_2/baseline.[1-22] ... (ldscore_fromlist)
2025/12/26 11:52:50   -Read reference panel LD Scores for 1071448 SNPs.
2025/12/26 11:52:50   -Removing partitioned LD Scores with zero variance.
2025/12/26 11:52:50   -Reading regression weight LD Score from /home/yunye/tools/ldsc/ldscores/eas_weights/weights.EAS.hm3_noMHC.[1-22] ... (ldscore_fromlist)
2025/12/26 11:52:51   -Read regression weight LD Scores for 1071448 SNPs.
2025/12/26 11:52:52   -After merging with reference panel LD, 1061153 SNPs remain.
2025/12/26 11:52:53   -After merging with regression SNP LD, 1061153 SNPs remain.
2025/12/26 11:52:53   -Removed 49 SNPs with chi^2 > 191.764 (1061104 SNPs remain)
2025/12/26 11:52:53   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.1.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:52:55   -Performing regression.
2025/12/26 11:52:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.2.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:00   -Performing regression.
2025/12/26 11:53:02   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.3.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:04   -Performing regression.
2025/12/26 11:53:06   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.4.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:09   -Performing regression.
2025/12/26 11:53:10   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.5.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:13   -Performing regression.
2025/12/26 11:53:15   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.6.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:17   -Performing regression.
2025/12/26 11:53:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.7.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:22   -Performing regression.
2025/12/26 11:53:24   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.8.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:26   -Performing regression.
2025/12/26 11:53:28   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.9.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:30   -Performing regression.
2025/12/26 11:53:32   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.10.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:34   -Performing regression.
2025/12/26 11:53:36   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.11.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:38   -Performing regression.
2025/12/26 11:53:40   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.12.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:42   -Performing regression.
2025/12/26 11:53:44   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.13.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:47   -Performing regression.
2025/12/26 11:53:49   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.14.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:51   -Performing regression.
2025/12/26 11:53:53   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.15.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:55   -Performing regression.
2025/12/26 11:53:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.16.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:53:59   -Performing regression.
2025/12/26 11:54:01   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.17.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:04   -Performing regression.
2025/12/26 11:54:06   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.18.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:08   -Performing regression.
2025/12/26 11:54:10   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.19.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:12   -Performing regression.
2025/12/26 11:54:14   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.20.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 11:54:17   -Performing regression.
2025/12/26 11:54:18   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.21.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:21   -Performing regression.
2025/12/26 11:54:23   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.22.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:25   -Performing regression.
2025/12/26 11:54:27   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.23.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:29   -Performing regression.
2025/12/26 11:54:31   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.24.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:33   -Performing regression.
2025/12/26 11:54:35   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.25.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:37   -Performing regression.
2025/12/26 11:54:40   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.26.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:42   -Performing regression.
2025/12/26 11:54:44   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.27.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:46   -Performing regression.
2025/12/26 11:54:48   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.28.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:50   -Performing regression.
2025/12/26 11:54:52   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.29.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:54   -Performing regression.
2025/12/26 11:54:56   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.30.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:54:58   -Performing regression.
2025/12/26 11:55:00   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.31.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:03   -Performing regression.
2025/12/26 11:55:05   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.32.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:07   -Performing regression.
2025/12/26 11:55:09   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.33.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:11   -Performing regression.
2025/12/26 11:55:14   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.34.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:16   -Performing regression.
2025/12/26 11:55:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.35.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:21   -Performing regression.
2025/12/26 11:55:23   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.36.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:25   -Performing regression.
2025/12/26 11:55:27   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.37.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:29   -Performing regression.
2025/12/26 11:55:31   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.38.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:34   -Performing regression.
2025/12/26 11:55:36   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.39.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:38   -Performing regression.
2025/12/26 11:55:40   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.40.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:42   -Performing regression.
2025/12/26 11:55:44   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.41.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:47   -Performing regression.
2025/12/26 11:55:49   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.42.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:51   -Performing regression.
2025/12/26 11:55:53   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.43.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:55:55   -Performing regression.
2025/12/26 11:55:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.44.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:00   -Performing regression.
2025/12/26 11:56:02   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.45.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:04   -Performing regression.
2025/12/26 11:56:07   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.46.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:09   -Performing regression.
2025/12/26 11:56:11   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.47.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 11:56:13   -Performing regression.
2025/12/26 11:56:15   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.48.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:18   -Performing regression.
2025/12/26 11:56:20   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.49.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:22   -Performing regression.
2025/12/26 11:56:24   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.50.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:26   -Performing regression.
2025/12/26 11:56:28   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.51.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:30   -Performing regression.
2025/12/26 11:56:32   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.52.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:35   -Performing regression.
2025/12/26 11:56:37   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.53.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/GTEx.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:39   -Performing regression.
2025/12/26 11:56:41   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.1.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:43   -Performing regression.
2025/12/26 11:56:45   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.2.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:47   -Performing regression.
2025/12/26 11:56:49   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.3.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:52   -Performing regression.
2025/12/26 11:56:53   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.4.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:56:56   -Performing regression.
2025/12/26 11:56:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.5.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:00   -Performing regression.
2025/12/26 11:57:01   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.6.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:04   -Performing regression.
2025/12/26 11:57:06   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.7.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:08   -Performing regression.
2025/12/26 11:57:10   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.8.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:12   -Performing regression.
2025/12/26 11:57:14   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.9.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:16   -Performing regression.
2025/12/26 11:57:18   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.10.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:21   -Performing regression.
2025/12/26 11:57:22   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.11.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:25   -Performing regression.
2025/12/26 11:57:27   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.12.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:29   -Performing regression.
2025/12/26 11:57:31   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.13.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:33   -Performing regression.
2025/12/26 11:57:35   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.14.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:37   -Performing regression.
2025/12/26 11:57:39   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.15.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:42   -Performing regression.
2025/12/26 11:57:44   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.16.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:46   -Performing regression.
2025/12/26 11:57:48   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.17.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:50   -Performing regression.
2025/12/26 11:57:52   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.18.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:55   -Performing regression.
2025/12/26 11:57:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.19.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:57:59   -Performing regression.
2025/12/26 11:58:01   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.20.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:03   -Performing regression.
2025/12/26 11:58:05   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.21.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 11:58:08   -Performing regression.
2025/12/26 11:58:10   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.22.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:13   -Performing regression.
2025/12/26 11:58:15   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.23.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:17   -Performing regression.
2025/12/26 11:58:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.24.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:22   -Performing regression.
2025/12/26 11:58:25   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.25.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:27   -Performing regression.
2025/12/26 11:58:29   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.26.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:31   -Performing regression.
2025/12/26 11:58:33   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.27.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:36   -Performing regression.
2025/12/26 11:58:38   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.28.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:41   -Performing regression.
2025/12/26 11:58:43   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.29.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:46   -Performing regression.
2025/12/26 11:58:48   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.30.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:50   -Performing regression.
2025/12/26 11:58:52   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.31.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:55   -Performing regression.
2025/12/26 11:58:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.32.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:58:59   -Performing regression.
2025/12/26 11:59:01   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.33.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:04   -Performing regression.
2025/12/26 11:59:06   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.34.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:08   -Performing regression.
2025/12/26 11:59:10   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.35.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:13   -Performing regression.
2025/12/26 11:59:15   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.36.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:17   -Performing regression.
2025/12/26 11:59:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.37.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:21   -Performing regression.
2025/12/26 11:59:23   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.38.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:26   -Performing regression.
2025/12/26 11:59:28   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.39.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:30   -Performing regression.
2025/12/26 11:59:32   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.40.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:34   -Performing regression.
2025/12/26 11:59:36   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.41.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:38   -Performing regression.
2025/12/26 11:59:40   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.42.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:42   -Performing regression.
2025/12/26 11:59:44   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.43.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:47   -Performing regression.
2025/12/26 11:59:48   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.44.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:51   -Performing regression.
2025/12/26 11:59:53   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.45.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:55   -Performing regression.
2025/12/26 11:59:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.46.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 11:59:59   -Performing regression.
2025/12/26 12:00:01   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.47.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:04   -Performing regression.
2025/12/26 12:00:07   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.48.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 12:00:10   -Performing regression.
2025/12/26 12:00:12   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.49.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:14   -Performing regression.
2025/12/26 12:00:16   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.50.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:19   -Performing regression.
2025/12/26 12:00:21   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.51.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:24   -Performing regression.
2025/12/26 12:00:26   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.52.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:29   -Performing regression.
2025/12/26 12:00:31   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.53.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:34   -Performing regression.
2025/12/26 12:00:37   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.54.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:39   -Performing regression.
2025/12/26 12:00:42   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.55.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:44   -Performing regression.
2025/12/26 12:00:47   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.56.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:49   -Performing regression.
2025/12/26 12:00:52   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.57.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:00:54   -Performing regression.
2025/12/26 12:00:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.58.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:00   -Performing regression.
2025/12/26 12:01:02   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.59.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:05   -Performing regression.
2025/12/26 12:01:08   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.60.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:11   -Performing regression.
2025/12/26 12:01:13   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.61.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:16   -Performing regression.
2025/12/26 12:01:18   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.62.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:21   -Performing regression.
2025/12/26 12:01:23   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.63.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:25   -Performing regression.
2025/12/26 12:01:28   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.64.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:30   -Performing regression.
2025/12/26 12:01:33   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.65.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:35   -Performing regression.
2025/12/26 12:01:38   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.66.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:41   -Performing regression.
2025/12/26 12:01:43   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.67.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:47   -Performing regression.
2025/12/26 12:01:49   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.68.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:53   -Performing regression.
2025/12/26 12:01:55   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.69.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:01:59   -Performing regression.
2025/12/26 12:02:01   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.70.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:04   -Performing regression.
2025/12/26 12:02:07   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.71.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:10   -Performing regression.
2025/12/26 12:02:13   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.72.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:15   -Performing regression.
2025/12/26 12:02:18   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.73.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:21   -Performing regression.
2025/12/26 12:02:24   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.74.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:27   -Performing regression.
2025/12/26 12:02:29   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.75.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 12:02:32   -Performing regression.
2025/12/26 12:02:34   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.76.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:37   -Performing regression.
2025/12/26 12:02:40   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.77.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:43   -Performing regression.
2025/12/26 12:02:45   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.78.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:47   -Performing regression.
2025/12/26 12:02:50   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.79.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:52   -Performing regression.
2025/12/26 12:02:54   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.80.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:02:57   -Performing regression.
2025/12/26 12:03:00   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.81.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:02   -Performing regression.
2025/12/26 12:03:04   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.82.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:06   -Performing regression.
2025/12/26 12:03:08   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.83.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:10   -Performing regression.
2025/12/26 12:03:12   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.84.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:15   -Performing regression.
2025/12/26 12:03:17   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.85.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:19   -Performing regression.
2025/12/26 12:03:21   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.86.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:23   -Performing regression.
2025/12/26 12:03:25   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.87.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:27   -Performing regression.
2025/12/26 12:03:29   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.88.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:32   -Performing regression.
2025/12/26 12:03:34   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.89.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:36   -Performing regression.
2025/12/26 12:03:38   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.90.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:40   -Performing regression.
2025/12/26 12:03:42   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.91.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:44   -Performing regression.
2025/12/26 12:03:46   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.92.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:48   -Performing regression.
2025/12/26 12:03:50   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.93.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:53   -Performing regression.
2025/12/26 12:03:55   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.94.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:03:57   -Performing regression.
2025/12/26 12:03:59   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.95.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:01   -Performing regression.
2025/12/26 12:04:03   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.96.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:06   -Performing regression.
2025/12/26 12:04:08   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.97.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:10   -Performing regression.
2025/12/26 12:04:12   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.98.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:15   -Performing regression.
2025/12/26 12:04:17   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.99.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:19   -Performing regression.
2025/12/26 12:04:21   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.100.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:23   -Performing regression.
2025/12/26 12:04:26   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.101.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:28   -Performing regression.
2025/12/26 12:04:30   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.102.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 12:04:33   -Performing regression.
2025/12/26 12:04:35   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.103.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:37   -Performing regression.
2025/12/26 12:04:39   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.104.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:42   -Performing regression.
2025/12/26 12:04:44   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.105.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:47   -Performing regression.
2025/12/26 12:04:49   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.106.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:51   -Performing regression.
2025/12/26 12:04:54   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.107.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:04:56   -Performing regression.
2025/12/26 12:04:59   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.108.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:01   -Performing regression.
2025/12/26 12:05:04   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.109.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:06   -Performing regression.
2025/12/26 12:05:09   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.110.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:12   -Performing regression.
2025/12/26 12:05:14   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.111.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:17   -Performing regression.
2025/12/26 12:05:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.112.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:21   -Performing regression.
2025/12/26 12:05:24   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.113.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:26   -Performing regression.
2025/12/26 12:05:29   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.114.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:32   -Performing regression.
2025/12/26 12:05:35   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.115.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:38   -Performing regression.
2025/12/26 12:05:41   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.116.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:43   -Performing regression.
2025/12/26 12:05:46   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.117.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:49   -Performing regression.
2025/12/26 12:05:52   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.118.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:05:55   -Performing regression.
2025/12/26 12:05:57   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.119.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:00   -Performing regression.
2025/12/26 12:06:03   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.120.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:06   -Performing regression.
2025/12/26 12:06:08   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.121.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:11   -Performing regression.
2025/12/26 12:06:14   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.122.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:16   -Performing regression.
2025/12/26 12:06:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.123.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:22   -Performing regression.
2025/12/26 12:06:25   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.124.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:28   -Performing regression.
2025/12/26 12:06:31   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.125.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:33   -Performing regression.
2025/12/26 12:06:36   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.126.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:39   -Performing regression.
2025/12/26 12:06:41   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.127.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:45   -Performing regression.
2025/12/26 12:06:47   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.128.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:49   -Performing regression.
2025/12/26 12:06:52   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.129.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)

stdout:

2025/12/26 12:06:54   -Performing regression.
2025/12/26 12:06:56   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.130.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:06:59   -Performing regression.
2025/12/26 12:07:02   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.131.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:04   -Performing regression.
2025/12/26 12:07:07   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.132.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:09   -Performing regression.
2025/12/26 12:07:12   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.133.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:14   -Performing regression.
2025/12/26 12:07:17   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.134.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:20   -Performing regression.
2025/12/26 12:07:25   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.135.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:28   -Performing regression.
2025/12/26 12:07:31   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.136.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:34   -Performing regression.
2025/12/26 12:07:37   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.137.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:39   -Performing regression.
2025/12/26 12:07:42   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.138.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:44   -Performing regression.
2025/12/26 12:07:46   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.139.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:48   -Performing regression.
2025/12/26 12:07:50   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.140.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:52   -Performing regression.
2025/12/26 12:07:54   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.141.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:07:57   -Performing regression.
2025/12/26 12:07:59   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.142.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:01   -Performing regression.
2025/12/26 12:08:04   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.143.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:07   -Performing regression.
2025/12/26 12:08:09   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.144.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:12   -Performing regression.
2025/12/26 12:08:14   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.145.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:16   -Performing regression.
2025/12/26 12:08:19   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.146.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:21   -Performing regression.
2025/12/26 12:08:23   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.147.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:26   -Performing regression.
2025/12/26 12:08:28   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.148.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:30   -Performing regression.
2025/12/26 12:08:33   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.149.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:35   -Performing regression.
2025/12/26 12:08:37   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.150.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:40   -Performing regression.
2025/12/26 12:08:42   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.151.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:44   -Performing regression.
2025/12/26 12:08:46   -Reading cts reference panel LD Score from /home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.152.,/home/yunye/tools/ldsc/Multi_tissue_gene_expr_EAS_1000G_v3_ldscores/Franke.EAS.control.[1-22] ... (ldscore_fromlist)
2025/12/26 12:08:49   -Performing regression.
2025/12/26 12:08:51  -Results have been stored in .ldsc_partitioned_h2
2025/12/26 12:08:51 Finished running LD score regression.

Name	Coefficient	Coefficient_std_error	Coefficient_P_value
Pancreas	9.460678e-09	3.429194e-09	0.002900
A03.556.875.Upper.Gastrointestinal.Tract	9.761378e-09	4.007071e-09	0.007425
A03.556.124.526.767.Rectum	9.773394e-09	4.053364e-09	0.007950
A03.556.249.249.209.Cecum	9.289977e-09	3.977595e-09	0.009757
A03.556.875.875.Stomach	8.648790e-09	3.742879e-09	0.010424
...	...	...	...
A11.329.228.Fibroblasts	-6.156755e-09	2.852965e-09	0.984537
A10.615.550.Mucous.Membrane	-6.220756e-09	2.841565e-09	0.985709
Brain_Spinal_cord_(cervical_c-1)	-5.433865e-09	2.177073e-09	0.993719
A10.690.467.Muscle..Smooth	-7.479103e-09	2.721569e-09	0.997003
A07.541.510.110.Aortic.Valve	-7.363194e-09	2.520982e-09	0.998254

[205 rows x 4 columns]

Example

t2d.ldsc_h2_cts

Name	Coefficient	Coefficient_std_error	Coefficient_P_value
Pancreas	9.460678e-09	3.429194e-09	0.002900
A03.556.875.Upper.Gastrointestinal.Tract	9.761378e-09	4.007071e-09	0.007425
A03.556.124.526.767.Rectum	9.773394e-09	4.053364e-09	0.007950
A03.556.249.249.209.Cecum	9.289977e-09	3.977595e-09	0.009757
A03.556.875.875.Stomach	8.648790e-09	3.742879e-09	0.010424
...	...	...	...
A11.329.228.Fibroblasts	-6.156755e-09	2.852965e-09	0.984537
A10.615.550.Mucous.Membrane	-6.220756e-09	2.841565e-09	0.985709
Brain_Spinal_cord_(cervical_c-1)	-5.433865e-09	2.177073e-09	0.993719
A10.690.467.Muscle..Smooth	-7.479103e-09	2.721569e-09	0.997003
A07.541.510.110.Aortic.Valve	-7.363194e-09	2.520982e-09	0.998254

[205 rows x 4 columns]