Algorithm failed to converge after trying different initial values.

[anbai106]

Hey,

It seems that this error continuously occurs for most of my analyses:

Function arguments:
gwas1.df=~/trait1.data.wrangling.hdl.rds
gwas2.df=~/trait1.data.wrangling.hdl.rds
LD.path=~/UKBB_HapMap3_LD_reference
output.file=~/trait2_vs_trait1.Rout 

Loading GWAS1 ... 
Loading GWAS2 ... 

HDL: High-definition likelihood inference of genetic correlations and heritabilities (HDL)
Version 1.4.0 (2021-04-15) installed
Author: Zheng Ning, Xia Shen
Maintainer: Zheng Ning <zheng.ning@ki.se>

Tutorial: https://github.com/zhenin/HDL

Use citation("HDL") to know how to cite this work.

Analysis starts on Wed Oct 11 16:42:27 2023 
0 SNPs were removed in GWAS 1 due to missing N or missing test statistic.  
0 SNPs were removed in GWAS 2 due to missing N or missing test statistic.  
986178 out of 1029876 (95.76%) SNPs in reference panel are available in GWAS 1.  
986178 out of 1029876 (95.76%) SNPs in reference panel are available in GWAS 2.  
Warning: More than 1% SNPs in reference panel are missed in GWAS 1. This may generate bias in estimation. Please make sure that you are using correct reference panel.  
Warning: More than 1% SNPs in reference panel are missed in GWAS 2. This may generate bias in estimation. Please make sure that you are using correct reference panel.  
Estimation is ongoing ... 100%

Integrating piecewise results 
Error in HDL.rg(gwas1.df, gwas2.df, LD.path, Nref = Nref, N0 = N0, output.file = output.file,  : 
  Algorithm failed to converge after trying different initial values. 
Execution halted

The same analysis worked well with LDSC, though.

Can you please help???

This relates to two other tickets: #21 #6

Thanks

[gloriabenoit]

I had the same problem, sad to see it's still unanswered..