LD path problem

[aikedan]

Hi there~ I have a tough question. I'm using the Array LD reference panel, but when I complete all the steps and do the final HDL, it says, "It seems this directory does not contain all the files needed for HDL. Please check your LD path again. The current version of HDL only supports pre-computed LD reference panels." But I'm sure I downloaded all the files. Does anyone know what the problem is? Please tell me, I'd appreciate it.

[now2014]

• Step01: Verify the MD5 checksum of the downloaded UKB_array_SVD_eigen90_extraction.tar.gz file. It should be ff3fadd7ea08bd29759b6c652618cd1f.

• Step02: Ensure there are no errors during decompression. Use the following command:

  tar -xvf UKB_array_SVD_eigen90_extraction.tar.gz

• Step03: If the MD5 checksum is correct, check the contents of the uncompressed LD reference panel. Below are the expected contents of the /path/to/UKB_array_SVD_eigen90_extraction/ directory:

  $ tree /path/to/UKB_array_SVD_eigen90_extraction/
  UKB_array_SVD_eigen90_extraction/
  ├── ukb_array_chr10.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr10.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr11.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr11.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr1.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr12.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr12.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr1.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr13.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr13.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr1.3_n336000_500banded_90eigen.rda
  ├── ukb_array_chr14.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr14.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr15.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr15.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr16.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr16.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr17.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr17.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr18.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr19.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr20.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr21.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr2.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr22.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr2.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr2.3_n336000_500banded_90eigen.rda
  ├── ukb_array_chr3.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr3.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr3.3_n336000_500banded_90eigen.rda
  ├── ukb_array_chr4.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr4.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr5.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr5.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr6.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr6.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr6.3_n336000_500banded_90eigen.rda
  ├── ukb_array_chr7.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr7.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr8.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr8.2_n336000_500banded_90eigen.rda
  ├── ukb_array_chr9.1_n336000_500banded_90eigen.rda
  ├── ukb_array_chr9.2_n336000_500banded_90eigen.rda
  ├── ukb_chr10.1_n336000.bim
  ├── ukb_chr10.2_n336000.bim
  ├── ukb_chr11.1_n336000.bim
  ├── ukb_chr11.2_n336000.bim
  ├── ukb_chr1.1_n336000.bim
  ├── ukb_chr12.1_n336000.bim
  ├── ukb_chr12.2_n336000.bim
  ├── ukb_chr1.2_n336000.bim
  ├── ukb_chr13.1_n336000.bim
  ├── ukb_chr13.2_n336000.bim
  ├── ukb_chr1.3_n336000.bim
  ├── ukb_chr14.1_n336000.bim
  ├── ukb_chr14.2_n336000.bim
  ├── ukb_chr15.1_n336000.bim
  ├── ukb_chr15.2_n336000.bim
  ├── ukb_chr16.1_n336000.bim
  ├── ukb_chr16.2_n336000.bim
  ├── ukb_chr17.1_n336000.bim
  ├── ukb_chr17.2_n336000.bim
  ├── ukb_chr18.1_n336000.bim
  ├── ukb_chr19.1_n336000.bim
  ├── ukb_chr20.1_n336000.bim
  ├── ukb_chr21.1_n336000.bim
  ├── ukb_chr2.1_n336000.bim
  ├── ukb_chr22.1_n336000.bim
  ├── ukb_chr2.2_n336000.bim
  ├── ukb_chr2.3_n336000.bim
  ├── ukb_chr3.1_n336000.bim
  ├── ukb_chr3.2_n336000.bim
  ├── ukb_chr3.3_n336000.bim
  ├── ukb_chr4.1_n336000.bim
  ├── ukb_chr4.2_n336000.bim
  ├── ukb_chr5.1_n336000.bim
  ├── ukb_chr5.2_n336000.bim
  ├── ukb_chr6.1_n336000.bim
  ├── ukb_chr6.2_n336000.bim
  ├── ukb_chr6.3_n336000.bim
  ├── ukb_chr7.1_n336000.bim
  ├── ukb_chr7.2_n336000.bim
  ├── ukb_chr8.1_n336000.bim
  ├── ukb_chr8.2_n336000.bim
  ├── ukb_chr9.1_n336000.bim
  ├── ukb_chr9.2_n336000.bim
  ├── UKB_snp_counter_array.RData
  └── UKB_snp_list_array.vector_form.RData

• Step04: Ensure you run HDL using the directory /path/to/UKB_array_SVD_eigen90_extraction/, not the original compressed UKB_array_SVD_eigen90_extraction.tar.gz file.