StandAloneBlast is a module in BioPerl (www.bioperl.org) and therefore kind of a black box..
With that said, it should only return undef if the blast search that it did returns empty handed. But from doing the blast search manually (in my workaround) it can be seen that the search is not empty.

In reply to Re^2: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane
in thread BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane

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