Problem with mapping when using genome_resquiggle

[awjga]

Hi,

I have been running into a problem in mapping when using genome_resquiggle,
And this is the error message: Alignment not produced. Potentially failed to locate BWA index files.
And all my fast5 was not mapped.
I had used graphmap to map, is it the same with bwa.

To check if it was my there was issues with my data and reference genome, I had extracted the sequences out using poretools and mapped with graphmap directly.
I was able to map at least 12% of my total reads.

Is there anything I can do to map at least 12% of my reads with genome_resquiggle?
So that I can use nanoraw to analyze my data?