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NaN as depth value and temperature value

Hi,
I am finding some NaN values when examining the depth  and temp fields of the Ichthyop output. The values do not seem to affect the following time steps however. I have attached an image of the table, with drifter, lon, lat, depth and time as the column titles. 
 
Creating a shapefile and moving to GIS software is causing some problems with these NaN's as they are being assigned the value 1. Have I done something wrong in the simulation to generate these NaN values? 
Thanks,
John
 

Ichthyop version: 
Ichthyop 3.3alpha
Hydrodynamic dataset: 
ROMS 3D
Java version: 
Java SE 8
Operating system: 
Windows 10
Attachments: 

Hi John.

If its ok with you, could you please send me some forcing files and your configuration file, so that I can try to infer where these NaNs are coming from?

Thanks

Nicolas