"split chromosome" after sorting with bcftools

Question

[dec986]

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.