"intersect_assembly_errors" program runs too long a time without a finish

I want to compare assembly results from three assembly tools

1. I concat three assembly fasta to one;
2. running `intersect_assembly_errors ` with cmd 
```
intersect_assembly_errors -r ref.fasta -i ./all_assm.fa
```
but it is still running after more than 3 hour.

Is there something wrong with the process?