************************************************************

* ldsc_preprocess(ldsc_preprocess)

* Version 1.0

* (C)2018 Cue H. Lee

* Seoul National University

* Unlicensed software

************************************************************

Call:

./ldsc_preprocess.py \

--ref-ld-chr /lustre/xiongjy/GWAS_analysis_tools/pleio/ldsc/1000genome_ref/eur_w_ld_chr/ \

--out European_all \

--input input.txt \

--w-ld-chr /lustre/xiongjy/GWAS_analysis_tools/pleio/ldsc/1000genome_ref/eur_w_ld_chr/

Beginning analysis at Sat Nov 19 10:14:11 2022

Read 42 traits from input

Failed to create a directory at : European_all

Successfully created a directory at : European_all/temp

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Dividing z-scores with the correction factor (the squared root of the LDSC h2 analysis intercept value).

Generate input files (sumstats.txt.gz) for LDSC --rg analysis

Generated European_all/temp/stroke.sumstats.sumstats.gz

Generated European_all/temp/scz.sumstats.sumstats.gz

Generated European_all/temp/ptsd.sumstats.sumstats.gz

Generated European_all/temp/pd.sumstats.sumstats.gz

Generated European_all/temp/ocd.sumstats.sumstats.gz

Generated European_all/temp/ms.sumstats.sumstats.gz

Generated European_all/temp/migraine.sumstats.sumstats.gz

Generated European_all/temp/mdd.sumstats.sumstats.gz

Generated European_all/temp/Lewy_body_dementia.sumstats.sumstats.gz

Generated European_all/temp/Epilepsy.sumstats.sumstats.gz

Generated European_all/temp/cannabis_use_disorder.sumstats.sumstats.gz

Generated European_all/temp/asd.sumstats.sumstats.gz

Generated European_all/temp/Panic_disorder.sumstats.sumstats.gz

Generated European_all/temp/anorexia_nervosa.sumstats.sumstats.gz

Generated European_all/temp/als.sumstats.sumstats.gz

Generated European_all/temp/adhd.sumstats.sumstats.gz

Generated European_all/temp/ad.sumstats.sumstats.gz

Generated European_all/temp/bd.sumstats.sumstats.gz

Generated European_all/temp/uc.sumstats.sumstats.gz

Generated European_all/temp/Peritonitis.sumstats.sumstats.gz

Generated European_all/temp/Polyp_of_colon.sumstats.sumstats.gz

Generated European_all/temp/ibs.sumstats.sumstats.gz

Generated European_all/temp/ibd.sumstats.sumstats.gz

Generated European_all/temp/gu.sumstats.sumstats.gz

Generated European_all/temp/gred.sumstats.sumstats.gz

Generated European_all/temp/gastritis.sumstats.sumstats.gz

Generated European_all/temp/dyspepsia.sumstats.sumstats.gz

Generated European_all/temp/Inguinal_hernia.sumstats.sumstats.gz

Generated European_all/temp/fatty_liver_disease.sumstats.sumstats.gz

Generated European_all/temp/Oesophagitis.sumstats.sumstats.gz

Generated European_all/temp/duodenitis.sumstats.sumstats.gz

Generated European_all/temp/DU.sumstats.sumstats.gz

Generated European_all/temp/Diverticular_disease.sumstats.sumstats.gz

Generated European_all/temp/constipation.sumstats.sumstats.gz

Generated European_all/temp/colon_cancer.sumstats.sumstats.gz

Generated European_all/temp/Cholecystitis.sumstats.sumstats.gz

Generated European_all/temp/Cholelithiasis.sumstats.sumstats.gz

Generated European_all/temp/Primary_biliary_cholangitis.sumstats.sumstats.gz

Generated European_all/temp/cd.sumstats.sumstats.gz

Generated European_all/temp/Acute_appendicitis.sumstats.sumstats.gz

Generated European_all/temp/acute_pancreatitis.sumstats.sumstats.gz

Generated European_all/temp/Dysphagia.sumstats.sumstats.gz

Number of variants in common: 191167

Found 0 duplicated variants

Found no Allele mismatch

Final step: combine several summary statistical data

Summary of stroke:

Estimated alpha and theta for stroke: nan and nan

z-score (mean) -0.00722870990625

sample number (mean) 452043.598801

Summary of scz:

Estimated alpha and theta for scz: nan and nan

z-score (mean) -0.00142027271021

sample number (mean) 130643.743334

Summary of ptsd:

Estimated alpha and theta for ptsd: nan and nan

z-score (mean) 0.00138181676587

sample number (mean) 174477.880848

Summary of pd:

Estimated alpha and theta for pd: nan and nan

z-score (mean) -0.00744987866103

sample number (mean) 482730.0

Summary of ocd:

Estimated alpha and theta for ocd: nan and nan

z-score (mean) -0.00172807640505

sample number (mean) 14307.0

Summary of ms:

Estimated alpha and theta for ms: nan and nan

z-score (mean) 0.012915141686

sample number (mean) 115803.0

Summary of migraine:

Estimated alpha and theta for migraine: nan and nan

z-score (mean) 0.0180903947985

sample number (mean) 587834.656845

Summary of mdd:

Estimated alpha and theta for mdd: nan and nan

z-score (mean) 0.00241204218145

sample number (mean) 500199.0

Summary of Lewy_body_dementia:

Estimated alpha and theta for Lewy_body_dementia: nan and nan

z-score (mean) -0.0060952214447

sample number (mean) 6681.0

Summary of Epilepsy:

Estimated alpha and theta for Epilepsy: nan and nan

z-score (mean) 0.00337295725045

sample number (mean) 463010.0

Summary of cannabis_use_disorder:

Estimated alpha and theta for cannabis_use_disorder: nan and nan

z-score (mean) -0.00362981113327

sample number (mean) 356360.671779

Summary of asd:

Estimated alpha and theta for asd: nan and nan

z-score (mean) 0.00144409437369

sample number (mean) 55420.0

Summary of Panic_disorder:

Estimated alpha and theta for Panic_disorder: nan and nan

z-score (mean) 0.00148476005332

sample number (mean) 9907.0

Summary of anorexia_nervosa:

Estimated alpha and theta for anorexia_nervosa: nan and nan

z-score (mean) -0.00740174553668

sample number (mean) 72401.1805333

Summary of als:

Estimated alpha and theta for als: nan and nan

z-score (mean) -0.00193945218447

sample number (mean) 88544.9409678

Summary of adhd:

Estimated alpha and theta for adhd: nan and nan

z-score (mean) -0.000183026199266

sample number (mean) 52876.1748419

Summary of ad:

Estimated alpha and theta for ad: nan and nan

z-score (mean) -0.000323776745918

sample number (mean) 487385.345839

Summary of bd:

Estimated alpha and theta for bd: nan and nan

z-score (mean) 0.00252839999963

sample number (mean) 413395.197497

Summary of uc:

Estimated alpha and theta for uc: nan and nan

z-score (mean) 0.00428002669417

sample number (mean) 453080.799882

Summary of Peritonitis:

Estimated alpha and theta for Peritonitis: nan and nan

z-score (mean) 0.00142625547952

sample number (mean) 462933.0

Summary of Polyp_of_colon:

Estimated alpha and theta for Polyp_of_colon: nan and nan

z-score (mean) -0.00149473555547

sample number (mean) 463010.0

Summary of ibs:

Estimated alpha and theta for ibs: nan and nan

z-score (mean) 0.00473495795571

sample number (mean) 484209.712633

Summary of ibd:

Estimated alpha and theta for ibd: nan and nan

z-score (mean) -0.0115708591044

sample number (mean) 484598.0

Summary of gu:

Estimated alpha and theta for gu: nan and nan

z-score (mean) 0.00459513849905

sample number (mean) 453080.799882

Summary of gred:

Estimated alpha and theta for gred: nan and nan

z-score (mean) -0.0107571124695

sample number (mean) 55375.674018

Summary of gastritis:

Estimated alpha and theta for gastritis: nan and nan

z-score (mean) -0.000221979442759

sample number (mean) 453080.799882

Summary of dyspepsia:

Estimated alpha and theta for dyspepsia: nan and nan

z-score (mean) 0.00610172294871

sample number (mean) 463010.0

Summary of Inguinal_hernia:

Estimated alpha and theta for Inguinal_hernia: nan and nan

z-score (mean) -0.00500156104574

sample number (mean) 337199.0

Summary of fatty_liver_disease:

Estimated alpha and theta for fatty_liver_disease: nan and nan

z-score (mean) 0.00350481163214

sample number (mean) 778614.0

Summary of Oesophagitis:

Estimated alpha and theta for Oesophagitis: nan and nan

z-score (mean) -0.00130195356814

sample number (mean) 463010.0

Summary of duodenitis:

Estimated alpha and theta for duodenitis: nan and nan

z-score (mean) 0.00318724792541

sample number (mean) 453080.799882

Summary of DU:

Estimated alpha and theta for DU: nan and nan

z-score (mean) 0.0102599063155

sample number (mean) 361194.0

Summary of Diverticular_disease:

Estimated alpha and theta for Diverticular_disease: nan and nan

z-score (mean) -0.0051297597001

sample number (mean) 451099.0

Summary of constipation:

Estimated alpha and theta for constipation: nan and nan

z-score (mean) -0.00402821706501

sample number (mean) 453080.799882

Summary of colon_cancer:

Estimated alpha and theta for colon_cancer: nan and nan

z-score (mean) -0.00182668880396

sample number (mean) 453009.337061

Summary of Cholecystitis:

Estimated alpha and theta for Cholecystitis: nan and nan

z-score (mean) 0.0044830875898

sample number (mean) 361194.0

Summary of Cholelithiasis:

Estimated alpha and theta for Cholelithiasis: nan and nan

z-score (mean) 0.000138241098233

sample number (mean) 453080.799882

Summary of Primary_biliary_cholangitis:

Estimated alpha and theta for Primary_biliary_cholangitis: nan and nan

z-score (mean) -0.00170007391994

sample number (mean) 24510.0

Summary of cd:

Estimated alpha and theta for cd: nan and nan

z-score (mean) -0.00440297242292

sample number (mean) 453080.799882

Summary of Acute_appendicitis:

Estimated alpha and theta for Acute_appendicitis: nan and nan

z-score (mean) -0.00346875287407

sample number (mean) 453080.799882

Summary of acute_pancreatitis:

Estimated alpha and theta for acute_pancreatitis: nan and nan

z-score (mean) -0.00269449061387

sample number (mean) 453080.799882

Summary of Dysphagia:

Estimated alpha and theta for Dysphagia: nan and nan

z-score (mean) 0.00844731102995

sample number (mean) 453080.799882

Successfully removed the directory at : European_all/temp

Analysis finished at Sat Nov 19 13:34:14 2022

Total time elapsed: 3.0h:20.0m:2.63s