Problem with Reference and Query

[phrh]

Hi,
I want to use quickmerge with two assemblies A and B. If I understand right the merge genome will use the sequences from the query genome and try to bride those sequences by using the reference genome. However, when I use the assembly A as query and the B as reference I get the following error in the quickmerge step. Instead, when I use the assembly A as reference and the assembly B as query it does work. Do you have any idea what could it be?

terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr: __pos (which is 501) > this->size() (which is 0)
Aborted (core dumped)
./quickmerge -d $1.rq.delta -q $3 -r $2 -hco 5.0 -c 1.5 -l 300000 -ml 5000 -p quickmerge.$1