Hello, Drs. Shen and Ning:
I am reaching out to seek your assistance regarding an error I encountered while running the HDL.L.run.R script using the following command line:
Rscript XX/HDL.L.run.R
gwas1.df= XX/GWAS1.hdl.rds
gwas2.df= XX/GWAS2.hdl.rds
Trait1name="gwas1"
Trait2name="gwas2"
LD.path=XX/LD.path/
bim.path=XX/bimfile/
N0=0
output.file=XX/gwas1_gwas2.Rout
cores=5
type="WG"
save.path=XX/
I received the following error message:
"
Loading GWAS1 ...
Loading GWAS2 ...
Processing chromosome 1 region 1
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.
254 out of 254 (100%) SNPs in reference panel are available in GWAS 1.
254 out of 254 (100%) SNPs in reference panel are available in GWAS 2.
Error in region 1: object 'h11.hdl.cut' not found
"
and the same error also appeared for region2, region3, region 4 ......
To investigate further, I made two attempts. First, I tested the code for a single region. For example, when I ran chromosome 1 region 147, there was no error. However, for chromosome 1 region 14, I encountered the same 'h11.hdl.cut' error.
Second, I conducted a test using the UKB data from the tutorial, and it ran without reporting any errors. This makes me wonder if the problem might be caused by my own data. However, I did follow the "Format of summary statistics" section in the official tutorial to convert the format of my data, ensuring it aligns with the required specifications as much as possible.
I'm not sure why the 'h11.hdl.cut' object is not found. Could you please help me figure out the possible reasons for this error? Any guidance or suggestions on how to resolve it would be greatly appreciated.
Thanks so much!
Hello, Drs. Shen and Ning:
I am reaching out to seek your assistance regarding an error I encountered while running the HDL.L.run.R script using the following command line:
Rscript XX/HDL.L.run.R
gwas1.df= XX/GWAS1.hdl.rds
gwas2.df= XX/GWAS2.hdl.rds
Trait1name="gwas1"
Trait2name="gwas2"
LD.path=XX/LD.path/
bim.path=XX/bimfile/
N0=0
output.file=XX/gwas1_gwas2.Rout
cores=5
type="WG"
save.path=XX/
I received the following error message:
"
Loading GWAS1 ...
Loading GWAS2 ...
Processing chromosome 1 region 1
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.
254 out of 254 (100%) SNPs in reference panel are available in GWAS 1.
254 out of 254 (100%) SNPs in reference panel are available in GWAS 2.
Error in region 1: object 'h11.hdl.cut' not found
"
and the same error also appeared for region2, region3, region 4 ......
To investigate further, I made two attempts. First, I tested the code for a single region. For example, when I ran chromosome 1 region 147, there was no error. However, for chromosome 1 region 14, I encountered the same 'h11.hdl.cut' error.
Second, I conducted a test using the UKB data from the tutorial, and it ran without reporting any errors. This makes me wonder if the problem might be caused by my own data. However, I did follow the "Format of summary statistics" section in the official tutorial to convert the format of my data, ensuring it aligns with the required specifications as much as possible.
I'm not sure why the 'h11.hdl.cut' object is not found. Could you please help me figure out the possible reasons for this error? Any guidance or suggestions on how to resolve it would be greatly appreciated.
Thanks so much!