ftp vs https in downloading 1000 genome vcf file in Step 2_Population_stratification

[SarojaSomu]

Hi,

I noticed using the command wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz from the 2_Main_script_MDS.txt downloads a corrupted file. Hence creating plink files from the vcf resulted in file read failure error. But when ftp is replaced with https like this, wget https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz, there is no file corruption issue and the download is faster as well.

Thanks

[mpage21]

I was using that old ftp link as well and running into issues. Thank you for this insight!

[kuisu-GDUT]

Did anyone get the complete VCF file? I downloaded a 62G vcf.gz file, but it's incomplete/corrupted. help me!

wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz

64160300K .......... .......... .......... .......... ..........100% 1.19M 0s
64160350K .......... .......... .......... .......... ..........100% 1.19M 0s
64160400K .......... .......... .......... .......... ..........100% 1.16M 0s
64160450K .......... .......... .......... .......... ..........100% 1.19M 0s
64160500K ......                                                100% 1.36M=36m59s

2025-10-21 06:51:29 (1.19 MB/s) - 已关闭控制连接。
重试中。

--2025-10-21 07:06:39--  ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz
  (尝试次数：11) => ‘ALL.2of4intersection.20100804.genotypes.vcf.gz’
正在连接 ftp-trace.ncbi.nih.gov (ftp-trace.ncbi.nih.gov)|130.14.250.13|:21... 已连接。
正在以 anonymous 登录 ... 登录成功！
==> SYST ... 完成。    ==> PWD ... 完成。
==> TYPE I ... 完成。  ==> CWD (1) /1000genomes/ftp/release/20100804 ... 完成。
==> SIZE ALL.2of4intersection.20100804.genotypes.vcf.gz ... 65672092096
==> PASV ... 完成。    ==> REST 65700358468 ... 完成。
==> RETR ALL.2of4intersection.20100804.genotypes.vcf.gz ...
文件 ‘ALL.2of4intersection.20100804.genotypes.vcf.gz’ 不存在