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Question: Plink error File write failure
2
gravatar for lmobuchon
4.8 years ago by
lmobuchon • 40
lmobuchon • 40 wrote:

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

snp plink • 2.3k views
ADD COMMENT • link •
modified 2.0 years ago by zx8754 ♦ 9.9k • written 4.8 years ago by lmobuchon • 40
1
gravatar for Shab86
4.8 years ago by
Shab86 • 270
Helsinki
Shab86 • 270 wrote:

Do you have enough disk space/disk quota available for it? I think a file write failure is an indication of just that.
ADD COMMENT • link written 4.8 years ago by Shab86 • 270

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

ADD REPLY • link written 4.8 years ago by lmobuchon • 40

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

ADD REPLY • link written 4.8 years ago by Shab86 • 270
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