sex image.fits -c default.sex Before running sextractor, you need three files: default.sex - the config file mentioned above default.param - uncomment which parameters you want sextractor to output default.conv - a convolution mask... By default the output will be in a file called test.cat configurable in default.sex. These files must be in the same folder as your fits image unless you specify absolute paths. Get them with these commands: cp /usr/local/sextractor-2.19.5/config/default.sex . cp /usr/local/sextractor-2.19.5/config/default.param . cp /usr/local/sextractor-2.19.5/config/default.conv . You may also need: cp /usr/local/sextractor-2.19.5/config/default.nnw .