Hi,
Unfortunately there is no flag available on the PXI-5411 that indicates when the arbitrary sequence has finished. An alternative is to set up a marker that will send out a pulse when you have reached the end of the arbitrary sequence. With a marker you specify the location in number of samples. So if you know the length of the arbitrary sequence in samples then you can set a marker at the end of the sequence. To find out more details about using markers go to the NI Signal Generators Help document (Start >> Programs >> National Instruments >> NI-FGEN >> Documentation) In the Help document there are two sections with more information.
Fundamentals >> Arbitrary Waveform Generation Mode >> Marker Output Signal
and
Devices >> NI 5411 >> Waveform Generation >> Marker Events
Hope this helps!
Erick D
NI Applications Engineer