GO-Elite User Group Post Problem running GO-Elite on Mac

[Karen Clune]

Good morning,
I have been having problems running GO-Elite on a MacBook Pro (OS version 10.5.8).  I downloaded and installed the version for Leopard first.  Installation was successful, and I was able to download some databases.  When I tried to set up an analysis and select the input gene list directory, nothing would happen when I clicked on the "select folder" button.  I then installed the program version for Tiger, and got a little further.  I was able to set up and start an analysis, but then the program would crash.  The following messages would appear in the output window before the program crashed: 
 Importing previously parsed version of GO
GO categories imported and nested in 22 seconds
Performing mappfinder analysis on RI040110 denominator.txt

Thanks for any help you can provide.  Have a good day.

Regards,
Karen
kac...@nyp.org

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[Nathan Salomonis]

Hi Karen,

The first issue you report should be fixed in the next version to be released soon. Indeed, we will release a single Mac OSX version which should be compatible with all. As for the second issue, without a clear error it is unclear whether this is a Mac versus input file issue. When an error occurs, a log file should be saved to the output file you designated. My guess is that it is the latter. To verify, you can use our tutorial files and see if they give you the same problem (make sure to select mouse as the species). These files are found at http://groups.google.com/group/go-elite?hl=en. You can also email me the first few lines of your input and denominator files, for which I can confirm if there is an issue. Again, GO-Elite should complain if there is a specific issue, but appears not to be in the version you are using (1.20 of GO-Elite?).

You can also try the web service and see if this works at: http://webservices.rbvi.ucsf.edu/opal/GetServicesList.do

Please tell us how this goes.

Thanks,
Nathan

[KSC]

Hi Nathan,
Thanks for your reply. I'm using GO Elite version 1.20.
I used the tutorial files for practice right after installing the
program, and did not have any problems. However, when I tried running
the program this morning using the tutorial files, I had a problem
with the program crashing.

I tried using the web service and got the following message:
JobId : app1272639767267
Status code:4
Message:Cannot retrieve outputs after finish - Path contains invalid
character:
Output Base URL:http://webservices.rbvi.ucsf.edu:8080/app1272639767267

I checked for a log file in the output folder but the folder is empty.

Thanks again for your help.

Regards,
Karen
_________________________________________________________________
On Apr 29, 1:02 pm, Nathan Salomonis <nsalomo...@gladstone.ucsf.edu>
wrote:

> Hi Karen,
>
> The first issue you report should be fixed in the next version to be
> released soon. Indeed, we will release a single Mac OSX version which should
> be compatible with all. As for the second issue, without a clear error it is
> unclear whether this is a Mac versus input file issue. When an error occurs,
> a log file should be saved to the output file you designated. My guess is
> that it is the latter. To verify, you can use our tutorial files and see if
> they give you the same problem (make sure to select mouse as the species).

> These files are found athttp://groups.google.com/group/go-elite?hl=en. You

> can also email me the first few lines of your input and denominator files,
> for which I can confirm if there is an issue. Again, GO-Elite should
> complain if there is a specific issue, but appears not to be in the version
> you are using (1.20 of GO-Elite?).
>
> You can also try the web service and see if this works at:http://webservices.rbvi.ucsf.edu/opal/GetServicesList.do
>
> Please tell us how this goes.
>
> Thanks,
> Nathan
>

> On 4/29/10 7:44 AM, "Karen Clune" <kac9...@nyp.org> wrote:
>
>
>
> > Good morning,
> > I have been having problems running GO-Elite on a MacBook Pro (OS version
> > 10.5.8).  I downloaded and installed the version for Leopard first. 
> > Installation was successful, and I was able to download some databases.  When
> > I tried to set up an analysis and select the input gene list directory,
> > nothing would happen when I clicked on the "select folder" button.  I then
> > installed the program version for Tiger, and got a little further.  I was able
> > to set up and start an analysis, but then the program would crash.  The
> > following messages would appear in the output window before the program
> > crashed: 
> >  Importing previously parsed version of GO
> > GO categories imported and nested in 22 seconds
> > Performing mappfinder analysis on RI040110 denominator.txt
>
> > Thanks for any help you can provide.  Have a good day.
>
> > Regards,
> > Karen

> > kac9...@nyp.org

[Nathan Salomonis]

Hi Karen,

Thanks for the sending the output and this current bug. Your input files
look good so I would try this on the webserver and see how it goes after
noting the below filename syntax.

We are familiar with this webserver bug occurring if there are spaces in the
file name for the input and denominator files. I will fix this ASAP, but in
the meantime, just replace spaces in the filename with underscores.
Best,
Nathan