Problem with .bed file

Question

[Dinmukhamed]

I have problem with converting .map and .ped file to .bed file. Map and ped files are without any problems but when code was done it gave corrupted .bed file.

$ ./plink.exe --file across --dog --make-bed --out across_data
PLINK v1.90b7.2 64-bit (11 Dec 2023)           www.cog-genomics.org/plink/1.9/
(C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to across_data.log.
Options in effect:
  --dog
  --file across
  --make-bed
  --out across_data

16221 MB RAM detected; reserving 8110 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (46 variants, 1572 dogs).
--file: across_data-temporary.bed + across_data-temporary.bim +
across_data-temporary.fam written.
46 variants loaded from .bim file.
1572 dogs (666 males, 906 females) loaded from .fam.
1570 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 1572 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.985037.
46 variants and 1572 dogs pass filters and QC.
Among remaining phenotypes, 751 are cases and 819 are controls.  (2 phenotypes
are missing.)
--make-bed to across_data.bed + across_data.bim + across_data.fam ... done.

Then it gave text like this

[Pierre Lindenbaum]

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Answer 1

[Pierre Lindenbaum]

Then it gave text like thi

plink bed is NOT a text file but a binary format. https://www.cog-genomics.org/plink/1.9/formats#bed