Bedtools intersect error at the end of funannote predict

[jaylward2]

Running funannotate v1.8.17 in a conda environment
Bedtools v2.31.1 (also tried downgrading to 2.31.0 and 2.29.0)

funannotate predict -i genome.masked --out genome_funannotate --species “species_name” --strain number --name “locus_tag” --cpus 10

After printing "Generating GenBank tbl annotation file" an error occurs with the command
bedtools intersect -a tmp.exon.2185454.bed -u -f 0.9 -s -b genome_funannotate/predict_misc/protein_alignments.gff3

Running the command above on its own returns "Error: Unable to determine type for file tmp.exon.2185454.bed"

Some google searches told me that this might be due to the start position number being lower than the end position, which I tested with:
awk '{if ($2 > $3) print $1"\t"$3"\t"$2; else print $1"\t"$2"\t"$3}' tmp.exon.2185454.bed > new.bed

Using the new bed file to run bedtools intersect -a new.bed -u -f 0.9 -s -b genome_funannotate/predict_misc/protein_alignments.gff3
does not return an error (actually gives no output). So it seems to solve the problem, but does not really help since I don't know how to incorporate it into the funannotate predict pipeline.

Any suggestions?

The logfile, the offending .bed file and the output of funannotate check --show-versions are attached
funannotate_check.txt
funannotate-predict.log
tmp.exon.2185454.bed.txt