Plink2 failed to open VCF file

Ciaran Kelly

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Mar 13, 2019, 8:58:53 AM3/13/19

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Hi, I am trying to use the --export haps command using plink2 on a vcf file but it fails to open the file

Even a simple command does not work:

plink2 --vcf chr.19_imputed_beagle_biallelic.vcf.gz.recode.vcf --geno --make-bed --out delete_this
PLINK v2.00a2 32-bit (22 Sep 2018) www.cog-genomics.org/plink/2.0/
(C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to delete_this.log.
Options in effect:
--geno
--make-bed
--out delete_this
--vcf chr.19_imputed_beagle_biallelic.vcf.gz.recode.vcf

Start time: Wed Mar 13 12:51:23 2019
1029911 MiB RAM detected; reserving 2047 MiB for main workspace.
Using up to 88 threads (change this with --threads).
Error: Failed to open chr.19_imputed_beagle_biallelic.vcf.gz.recode.vcf.
End time: Wed Mar 13 12:51:23 2019

However, Plink 1.9 works on the same file just fine (but I cant use the --export haps command using 1.9)

plink1.9 --vcf chr.19_imputed_beagle_biallelic.vcf.gz.recode.vcf --geno 0.1 --make-bed --out delete_this
PLINK v1.90b3.31 64-bit (3 Feb 2016) https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to delete_this.log.
Options in effect:
--geno 0.1
--make-bed
--out delete_this
--vcf chr.19_imputed_beagle_biallelic.vcf.gz.recode.vcf

1029911 MB RAM detected; reserving 514955 MB for main workspace.
--vcf: delete_this-temporary.bed + delete_this-temporary.bim +
delete_this-temporary.fam written.
696306 variants loaded from .bim file.
1502 people (0 males, 0 females, 1502 ambiguous) loaded from .fam.
Ambiguous sex IDs written to delete_this.nosex .
Using 1 thread (no multithreaded calculations invoked.
Before main variant filters, 1502 founders and 0 nonfounders present.
Calculating allele frequencies... done.
0 variants removed due to missing genotype data (--geno).
696306 variants and 1502 people pass filters and QC.
Note: No phenotypes present.
--make-bed to delete_this.bed + delete_this.bim + delete_this.fam ... done.

Some other VCF files do work under this command on Plink2 so I am unsure what the problem is. Can anyone help?

Thank you.

Christopher Chang

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Mar 13, 2019, 10:44:05 AM3/13/19

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Might be a bug in the 32-bit build, which gets about 10000x less testing than the 64-bit builds. Can you try rerunning with the latest 64-bit build?

(Meanwhile, if this still fails with the latest 32-bit build, I’ll investigate the bug; what operating system is this on?)

Message has been deleted

Ciaran Kelly

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Mar 13, 2019, 11:37:35 AM3/13/19

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Thank you, it could read the vcf file using PLINK v2.00a2LM 64-bit Intel (9 Mar 2019). The operating system is Ubuntu 16.04.3 LTS. For some reason I cannot download the latest 32 bit build to check if its still a problem there using http://s3.amazonaws.com/plink2-assets/plink2_linux_i686_20190309.zip on https://www.cog-genomics.org/plink/2.0/

Christopher Chang

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Mar 13, 2019, 12:01:22 PM3/13/19

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Oops, must have forgotten to upload that; will do so tonight.

Christopher Chang

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Mar 13, 2019, 5:52:51 PM3/13/19

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The 32-bit Linux binary is now posted.

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