The reference uploader job does not appear in the web-based jobs monitor
When mapping back to an assembly it is always worth considering the unmapped data. Epilogue and prologue sequence that is of significant length and does not map could be the result of the HQ region of the trace not being very accurate, and will likely occur in overloaded data. If a ZMW initially has two polymerases loaded the initial part of the trace can include cross talk from the two sequences, it is possible for one of the polymerases to stop sequencing and the trace will start to produce good sequence, if this point is not found accurately then a read can have 'junk' none mapping sequence in the epilogue or prologue. While you should be aware of this it is generally not a problem, and is accounted for in the HGAP assembly process. The bigger issue when aligning back to an assembly is the % of none mapping subreads, this can give an indication if the assembly accounts for all the underlying data. You should be looking for a mapping % of ~80-90% if this value is much lower then I would take a look at the unmapped_subreads file, and see if the unmapped data can be accounted for by the degenerage contigs, from CA, that are not included in the resequencing.
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