Here is a screen capture recording of my PTGui v6 workflow to make a panorama photographed with my Canon 5D and Canon 15mm FE lens. Note - I had already added alpha channels to the two nadir photographs, to remove the 360precision adjuste panorama tripod head side arm. So you see me select two .tif files for the nadir rather the two nadir .jpg files.
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Here is the resulting equirectangular image. Click on this image to see the Apple QTVR movie.