Plink error File write failure

Question

[lmobuchon]

Hi,

I tried to convert 1000genomes VCF to plink format using the command lines:

./plink --allow-no-sex --vcf ALL.chr10.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --make-bed --out chr10

But I had an error:

15970 MB RAM detected; reserving 2047 MB for main workspace.
--vcf: 3430k variants complete.
Error: File write failure.

I converted chromosomes 11 to Y without error but it is impossible for chromosomes 1 to 10. I have enough place (~800 Go) on my disk.

Thank you for help ! Lenha

Answer 1

[Shab86]

Do you have enough disk space/disk quota available for it? I think a file write failure is an indication of just that.

[lmobuchon]

Thank you ! Yes I checked it before lauching the analysis ! I have 800 Go available which is more than enough ! :)

[Shab86]

Read/write permissions not setup for the disk perhaps? Because the plink code shows the error (line 154): https://github.com/chrchang/plink-ng/blob/master/plink.c