"split chromosome" after sorting

[hhg7]

I'm running bcftools 1.15.1 on Linux 4.18.0-372.16.1.el8_6.x86_64 on Red Hat 8.6 (Ootpa) with gcc version 8.5.0 I am running bcftools in a series of commands

first I run bcftools sort and then

plink --bcf tmp.sort.bcf --allow-extra-chr --make-bed --out merged.eigenstrat.34string.length.vcf.gz

which works, and then

plink --bcf tmp.sort.bcf --allow-extra-chr --recode --out merged.eigenstrat.34string.length.vcf.gz

but then I get an error:

Error: .bim file has a split chromosome. Use --make-bed by itself to remedy this

this last error should have been remedied by bcftools sort but wasn't.

If I try to run the recode step based on the bed file, I get the error:

Options in effect:
  --allow-extra-chr
  --bed merged.eigenstrat.34string.length.vcf.gz
  --out merged.eigenstrat.34string.length.vcf.gz
  --recode

Error: A full .bed + .bim + .fam fileset is required for this.
For more information, try "plink --help <flag name>" or "plink --help | more".

How can I fix this error? sort didn't fix it, even though it should have.

or is this a problem with plink instead? I'm running PLINK v1.90b6.26 64-bit (2 Apr 2022)

[pd3]

You can check if the chromosomes are in single blocks with something like

bcftools query -f'%CHROM\n' file.bcf | uniq -c

Most likely not a problem with bcftools.

[pd3]

Since this is not a bcftools problem, I am closing the issue