Hi schroedj,
The scaffold.fasta should contain the most contiguous sequence that the data and algorithm is able to generate. If it isn't "one long fasta sequence" then you need to look into why you're getting the results you are getting, or if AHA is making any difference. There should be very basic stats on the number of scaffolds created, which you can compare to the number of contigs you supplied. Is this what you are asking about?
We look at:
How large is the genome you are trying to assemble? (AHA is only supported up to 200Mb)
How "good" are the contigs going into the AHA? (number of contigs, contig lengths, %of genome, etc.)
How much PacBio Data are you supplying? (My personal rule-of thumb is to give AHA at least 5x coverage, but 2x coverage is the minimum to get any results at all. That is because the "redundancy" parameter is set to 2 by default. This is the minimum number of reads needed to link two contigs).
The parameters to tune AHA can be found in the smrtpipe reference guide:
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Working with PacBio AHA output
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