Error: Random File read failure (PLINK v1.90b4.1 64-bit (30 Mar 2017) )

[Mike Dacre]

Having a strange file read failure.

plink \

--bfile /godot/1000genomes/1000GP_Phase3/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes \

--ld-snp rs9273445 \

--r2 in-phase dprime \

--snps rs9273445 rs11568830 rs11568831 rs28746851 rs9271685 rs9271689 rs9272416 rs9274407 rs9274529 rs9274654 rs9274655 rs9274656 rs9274660 rs9271488 rs9271640 rs9271720

Works fine

plink \

--bfile /godot/1000genomes/1000GP_Phase3/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes \

--ld-snp rs9273445 \

--r2 in-phase dprime \

--snps rs9273445 rs9272346 rs1063355 rs28383344 rs2858864 rs3828800 rs532098 rs674313 rs9271408 rs9271488 rs9271640 rs9271720 rs9271775 rs9274407

Fails with:

PLINK v1.90b4.1 64-bit (30 Mar 2017)           www.cog-genomics.org/plink/1.9/

(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to plink.log.

Options in effect:

  --bfile /godot/1000genomes/1000GP_Phase3/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes

  --ld-snp rs9273445

  --r2 in-phase dprime

  --snps rs9273445 rs9272346 rs1063355 rs28383344 rs2858864 rs3828800 rs532098 rs674313 rs9271408 rs9271488 rs9271640 rs9271720 rs9271775 rs9274407

32119 MB RAM detected; reserving 16059 MB for main workspace.

Allocated 1606 MB successfully, after larger attempt(s) failed.

14 out of 4997829 variants loaded from .bim file.

2504 people (0 males, 0 females, 2504 ambiguous) loaded from .fam.

Ambiguous sex IDs written to plink.nosex .

Using up to 8 threads (change this with --threads).

Before main variant filters, 2504 founders and 0 nonfounders present.

Calculating allele frequencies... done.

14 variants and 2504 people pass filters and QC.

Note: No phenotypes present.

--r2 in-phase dprime... 0% [processing]

Error: File read failure.

Removing the last three snps in --snps seems to fix the error, but it isn't just a number of snps issue, because the top one works fine. Also, reshuffling the snps in the non-working version doesn't change anything.

The file is the 1000genomes chromosome 6 file. I only ever get this error with this file, the other chromosome files work fine. However, I expect more snps on chromosome 6 because of the HLA, so it might just be a numbers thing.

The bfile is built with:

i=ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz;

j=$(echo $i | sed 's/.vcf.gz//');

vftools --gzvcf $i --plink-tped --out $j &&

plink --tped $j.tped --tfam $j.tfam --out $j

I tried doing that a few times, it doesn't fix the issue. The VCF is straight of the EBI server.

Not sure how to go about debugging this. Any suggestions?

Thanks!

[Christopher Chang]

That's probably a --ld-snp bug.  I'll try to replicate the crash on my own; if I fail to do so, I'll post a debug build with extra logging around all the places --r2 might throw a read-failure error.

[Mike Dacre]

Great, thanks.

[Christopher Chang]

This bug should be fixed in the May 7 builds; let me know if you run into any more problems.

On Friday, May 5, 2017 at 3:24:31 PM UTC-7, Mike Dacre wrote:

[Mike Dacre]

Yup, that fixed it, thanks so much!

[ga...@igib.in]

Hi Chang

I want to convert 1000 genome phase 3 data (vcf format files-.vcf.gz) to plink format files .bed , .bim and .fam. I downloaded plink 1.9 and applied following commands:

plink --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated.genotypes.vcf.gz --keep-allele-order --biallelic-only --vcf-filter --vcf-require-gt --make-bed --out CHR_1_PLINK_1000GP3

When I run this command, I get

32072 MB RAM detected; reserving 16036 MB for main workspace
--vcf: 2199k variants complete.
Error: File read failure.

I get the same error even when I just want to read my vcf file through plink using following command:

plink --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated.genotypes.vcf.gz

When I tried to uncompress my file before conversion, uncompression throwd an error.

Any suggestions?

[Christopher Chang]

Are other programs (e.g. bcftools) able to process the compressed VCF? If not, the file may be corrupted and you need to re-download it.

[ga...@igib.in]

Hi Chang, the file was corrupted. I downloaded it again and re-ran the command. Command worked fine this time.


Gauri

[Gauri Prasad]

Hi I want to merge two 1000 genome phase 3 files of different chromosomes. I used plink v1.9 .

I applied following command:

plink --bfile chr1 --bmerge chr2.bed chr2.bim chr2.fam --make-bed --out merge1_2

It was found that around 11000 markers have same genetic position

And then it showed file read error. What could be the reason and how to solve it. Should I remove those markers or they could be also important downstream analysis. What should I do?

Gauri

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