Non-interactive mode and errors

[Andrey Rozenberg]

The --quiet option doesn't prevent the program from prompting for user input in case of an error:

$ cat test.phy
 1 1
A  G
$ codonphyml -i test.phy --quiet


Option for frequency (-f option) not set; assume empirical frequencies.

. Err: we need at least 3 sequences to analyze.

. Type enter to exit.

In my particular bash pipeline the problem manifested itself in a very unexpected way. The only workaround for now is sending one or better infinite number of line feeds:

echo | codonphyml -i test.phy --quiet
yes "" | codonphyml -i test.phy --quiet

[Marcelo S Zanetti]

Hi Andrey. Thank you for your feedback. I will redirect the error messages to a log file when --quiet is enabled. If you have any other inquires let me know! Best.