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I have written a .cl script that I am using for photometry and data processing. I have the two lines of code near the end. When I run the code, the first one (daofind) runs, but the second one (phot) does not run. I tried commenting out daofind, and when I do that it tires to run phot, which does not work because the coords file does not exist. Does anyone have a clue as to why this would happen?
daofind HDcomb.fits output="HDcomb.imh.coo"
phot HDcomb.fits coords="HDcomb.imh.coo" output="HDcomb.mag"

If this is a .cl file of commands you execute by indirection rather than a procedure script, then its likely the problem is that with this method ALL input is taken from the script file. If the daophot.verify package parameter is set then you may be getting extra prompts that are being answered by your phot command in the script file.You can try turning off this parameter, or else turn the .cl into a procedure script and execute it as a task.