1. Problem, the following problem occurred inexplicably. After tossing for a long time, I didn’t find out the reason. Later, I simply solved it by violence. I directly decompressed the file to see what happened. After decompressing for a long time, it prompted that the file was damaged,….

Error: File read failure.

2. Download the file again and test

root@PC1:/home/GWA_tutorial/2_Population_stratification#plink --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes
PLINK v1.90b6.24 64-bit (6 Jun 2021)           www.cog-genomics.org/plink/1.9/
(C) 2005-2021 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to ALL.2of4intersection.20100804.genotypes.log.
Options in effect:
  --make-bed
  --out ALL.2of4intersection.20100804.genotypes
  --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz

15974 MB RAM detected; reserving 7987 MB for main workspace.
--vcf: ALL.2of4intersection.20100804.genotypes-temporary.bed +
ALL.2of4intersection.20100804.genotypes-temporary.bim +
ALL.2of4intersection.20100804.genotypes-temporary.fam written.
25488488 variants loaded from .bim file.
629 people (0 males, 0 females, 629 ambiguous) loaded from .fam.
Ambiguous sex IDs written to ALL.2of4intersection.20100804.genotypes.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 629 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.615305.
25488488 variants and 629 people pass filters and QC.
Note: No phenotypes present.
--make-bed to ALL.2of4intersection.20100804.genotypes.bed +
ALL.2of4intersection.20100804.genotypes.bim +
ALL.2of4intersection.20100804.genotypes.fam ... done.

There was no error this time.

Error: file read failure error occurs when Plink processes large files One possibility is file corruption!