bgen read failure: Input/output error.
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Sandra Barral
Apr 28, 2022, 12:02:10 PM4/28/22
to plink2-users
Hi All,
I am trying to convert bgen files into binary plink and for some of the chromosomes I keep getting an error
plink2 --bgen file.bgen ref-first --make-bed --out chr15_out --sample file.sample
Random number seed: 1651156828
257855 MiB RAM detected; reserving 128927 MiB for main workspace.
Allocated 40792 MiB successfully, after larger attempt(s) failed.
Using up to 40 threads (change this with --threads).
--bgen: 2767971 variants detected, format v1.2.
487409 samples imported from .sample file to temporary.psam .
Error: file.bgen read
failure: Input/output error.
257855 MiB RAM detected; reserving 128927 MiB for main workspace.
Allocated 40792 MiB successfully, after larger attempt(s) failed.
Using up to 40 threads (change this with --threads).
--bgen: 2767971 variants detected, format v1.2.
487409 samples imported from .sample file to temporary.psam .
Error: file.bgen read
failure: Input/output error.
Christopher Chang
Apr 28, 2022, 2:11:45 PM4/28/22
to plink2-users
Unfortunately, this error usually indicates a problem with your disk. Are you able to copy the file? If yes, does qctool -snp-stats work on it?
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