Default Exit value and command line options

Integrating mothur with other programs
1

Hi,

What is the default exit value of mothur if everything runs fine?

Are there some command line arguments I can specify?

Regards,

TL

2

Mothur does not have a error return code programmed in. We report errors in “human” form to the logfile and the screen. The error tag is [ERROR]. If you are searching a log file, it is also helpful to search for the quit command. If you don’t find it, that can indicate an error. Failure to find a quit command, usually indicate an error that caused a crash of mothur that bypassed our try catches, :oops: .

3

Hi,

Mothur does not have a error return code programmed in.

Hmmm I guess you don’t set one explicitly. Every program ( for unix/windows os ) returns an integer when the programm finished( by executing the last statement or by an error or cancelation ).

I use a special library for communicating with mothur ( ApacheCommons Exec ). There you can specify an integer for the app you want to start which the app returns when finishing( “normal” → without errors ).
I set this integer to 1 - which is the default return value for many applications if they finished correctly.

Regards,
TL

4

Re,

I set this integer to 1 - which is the default return value for many applications

:oops:
This is not true. I mixed something up … so I saw that you provide 0 as the default return code for a normal program termination.

Sorry,

TL