Command line mode doesn't return exit-code to indicate failure.

[bsmith89]

I'm trying to incorporate some mothur commands into a Makefile using the mothur "#some.command()" syntax (http://www.mothur.org/wiki/Command_line_mode).

At least for all of the examples I've tried (e.g. mothur "#not.a.command()"), the exit code is always 0. This leads to problems when the remaining steps in the pipeline execute.

I realize I'm trying to use mothur in a way it was not designed, but I'm hoping it's not a difficult patch. I'd also like a command-line option to turn off the welcome screen, but that's a different issue.

[bsmith89]

I see this has been discussed before: http://mothur.org/forum/viewtopic.php?f=10&t=2699

[pschloss]

Thanks Byron - we've been working on adding a few more command line options in the recent releases. We'll add a flag to remove the welcome screen. Also we'll have mothur rerun a 1 on successful completion and a 0 if there's an error.

We appreciate the suggestions!
Pat

[bsmith89]

Maybe that was a typo, but just in case: the normal "success" exit code on UNIX is 0, other numbers indicate failure.

[pschloss]

I see, you want it to be 1 if there's an error - right?

[bsmith89]

Yep, exactly. Some people will use different exit codes to mean different
things, but just returning "1" will work perfectly for my needs.

On Mon, Aug 24, 2015 at 2:04 PM, Pat Schloss notifications@github.com
wrote:

I see, you want it to be 1 if there's an error - right?

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#151 (comment).

[mothur-westcott]

If you want to skip the welcome screen you can run mothur in "quiet" mode.

./mothur "#myCommand(...);" -q

[bsmith89]

Oh, I didn't realize that. Thanks for the tip!

On Mon, Aug 24, 2015 at 2:12 PM, Sarah Westcott notifications@github.com
wrote:

If you want to skip the welcome screen you can run mothur in "quiet" mode.

./mothur "#myCommand(...);" -q

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#151 (comment).

[mooreryan]

I know this is an older issue, but I am running into the same problems as @bsmith89

[mothur-westcott]

Thanks for hitting this thread again, :). In version 1.37 we added output to the log file indicating the number of errors and warnings. The 1.38.0 branch includes the return codes you are looking for. If the log file indicates errors the return code will be set to 1, otherwise 0.