PLINK not converting entire vcf to bed file

Question

[ethan.kreuzer]

here is my code :

[ethan.kreuzer@hydra1 2_Population_stratification]$ plink --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes
[mii] Please select a module to run plink:
       MODULE                 PARENT(S)
    1  plink/1.9b_6.21-x86_64 StdEnv/2020
    2  plink/1.07             nixpkgs/16.09 intel/2018.3
    3  plink/1.9b_5.2-x86_64  nixpkgs/16.09
    4  plink/1.9b_4.1-x86_64  nixpkgs/16.09
Make a selection (1-4, q aborts) [1]: 1
[mii] loading StdEnv/2020 plink/1.9b_6.21-x86_64 ...
PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 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

50289 MB RAM detected; reserving 25144 MB for main workspace.
--vcf: 32k variants complete.
Error: File read failure.
[ethan.kreuzer@hydra1 2_Population_stratification]$ ls
1_Main_script_QC_GWAS.txt                    ALL.2of4intersection.20100804.genotypes-temporary.bed  ALL.2of4intersection.20100804.genotypes.vcf.gz  HapMap_3_r3_12.fam  MDS_merged.R  plink.fam
2_Main_script_MDS.txt                        ALL.2of4intersection.20100804.genotypes-temporary.bim  HapMap_3_r3_12.bed                              HapMap_3_r3_12.log  plink.bed     plink.log
ALL.2of4intersection.20100804.genotypes.log  ALL.2of4intersection.20100804.genotypes-temporary.fam  HapMap_3_r3_12.bim                              indepSNP.prune.in   plink.bim

Can someone help me understand how to convert the entire document vcf.gz file? Thank you

tutorial from : "https://github.com/MareesAT/GWA_tutorial/tree/master" in the "2_Population_stratification.zip" section

[GenoMax]

Error: File read failure.

Verify that your VCF file is readable all the way through and not corrupt/incomplete.

[ethan.kreuzer]

do you know how I could investigate this? I'm not sure what I should be looking for. Thank you for your reply.

[chrchang523]

I realize that it's not preinstalled on your system, but plink 2.0 provides a more useful error message here, and is generally a much better choice than plink 1.x for working with VCF data.