How to fix FreeBayes error "unable to find FASTA index entry for bed files"

Question

[wlei091226]

I'm trying to use freebayes to call variants through the following parameters using RNA-Seq data:

$freebayes --fasta-reference $ref \
--region $BED \
$bam \
> ${outdir}/${sample}.freebayes.vcf
and my bed files like this:
chr1:11868-12227
chr1:12612-12721
chr1:12974-13052
chr1:13220-14501
chr1:15004-15038
.....

but report an error:

unable to find FASTA index entry for '/path/to/GRCh38.exon.bed'

I'm pretty sure my fasta files have the index with the suffix .fai

Why did this happen?

[fra.r.silvestro]

I have the same issue. I check correspondence between fasta headers line and bed column. Both have chr1 as "prefix". May that fasta file has, other than Chr1 to Chr22, ChrM, Unknwon and HLA--### contigs while bed file not?