failed to open bed file
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Hello,
I am trying plink software to convert bed file to vcf file. But I am getting error.
The command:
plink --bfile [hglft_genome_470a4_43f4c0.bed] --recode vcf --out [outfile.vcf]
The error:
PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to i.log.
Options in effect:
--bfile [hglft_genome_470a4_43f4c0.bed]
--out i
--recode vcf
191830 MB RAM detected; reserving 95915 MB for main workspace.
Error: Failed to open [hglft_genome_470a4_43f4c0.bed].bed.
(TWAS) c506-003skx$ plink --bfile [hglft_genome_470a4_43f4c0] --recode vcf --out [outfile.vcf]
PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to i.log.
Options in effect:
--bfile [hglft_genome_470a4_43f4c0]
--out i
--recode vcf
191830 MB RAM detected; reserving 95915 MB for main workspace.
Error: Failed to open [hglft_genome_470a4_43f4c0].bed.
This is the content of my .bed file for reference:
chr22 15927338 15927339
chr22 15926767 15926768
chr22 15925769 15925770
chr22 15924807 15924808
chr22 15924146 15924147
chr22 15923295 15923296
chr22 15922887 15922888
chr22 15922875 15922876
chr22 15922837 15922838
chr22 15922096 15922097
chr22 15921734 15921735
chr22 15920797 15920798
chr22 15918255 15918256
chr22 15917692 15917693
chr22 15917389 15917390
chr22 15917224 15917225
chr22 15917199 15917200
chr22 15916940 15916941
chr22 15916940 15916941
chr22 15916817 15916818
chr22 15916706 15916707
chr22 15916309 15916310
chr22 15915686 15915687
chr22 15915652 15915653
chr22 15914587 15914588
chr22 15912242 15912243
chr22 15912242 15912243
chr22 15908475 15908476
chr22 15905975 15905976
chr22 15905929 15905930
Basic usage/troubleshooting questions should be posted to the plink2-users Google group, not here.