bedtools intersect -a A_input.bed -b B_input.bed ERROR: Received illegal bin number 37453 from getBin call. ERROR: Unable to add record to tree.
This seems to be due to the very large size of the barley chromosomes, which are up to almost 770 Mbp long. Curiously, when intersecting with the -sorted option, bedtools can handle the files. Using the -sorted option is recommended anyways, because it makes bedtools intersect faster and more memory efficient.
So, after sorting the files with
sort -k 1,1 -k2,2n input.bed
or the slower
bedtools sort input.bed
the intersection can be accomplished with
bedtools intersect -sorted -a A_input.bed -b B_input.bed
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