Hi Elizabeth, can you please let us know which parameters you have used? Thanks, Bjoern Am 18.10.2014 um 14:33 schrieb Elizabeth Chia:

...

Hi there

I'm running into this error with cuffdiff:

...

​​​​ I'm running galaxy locally on a cluster (1 head+3 compute nodes) with MySQL. Here's my hg summary:

...

​ Any clues?

I also keep getting the a similar 149 Internal Server error (with different Key Error) thrown when trying to install some tools. But strangely, after leaving it for awhile, it went back to normal. So I'm not too sure what's causing it.

Should I be updating galaxy to the latest stable one?

Please let me know if you require any other info.

Thanks!

liz

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hello Liz, I wish I had some better news - upgrading might help - we have definitely made modifications to that file since then - but not to address this issue I don't think. What would be really interesting is to see the Galaxy logs around the time of that error - I wonder if there would be some other exceptions logged that explains why that entry doesn't exist in the dictionary. I have seen errors like this caused by changing things around in the tool without modifying the version - I am assuming you haven't modified the cuffdiffs wrapper though? Ideally to track this down there would be a minimal example that can reproduce this problem - have this one dataset with this metadata in your history and run this cufflinks tool - but that would obviously be a lot of work on your part. If you did want to help debug this problem though - you could start a new history try opening the cuffdiff tool - verify it opens - and then slowly copy a few of that histories datasets at a time into the new history and try reopening the cuffdiff wrapper until you get an error. I would bet some combination of history dataset metadata is interacting with the cuffdiff wrapper. -John On Sun, Oct 26, 2014 at 11:26 PM, Elizabeth Chia <elchia@gmail.com> wrote:

Hi Bjorn

Thanks for getting back to me.

Sorry for the late reply. Was awaiting my user to get back to me.

It was the default cuffdiff parameters. If I'm not wrong, we keep experiencing this on/off with other tools too.

Appreciate any feedback and help. Thanks so much!

Best regards liz

On Sat, Oct 18, 2014 at 8:52 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

...

Hi Elizabeth,

can you please let us know which parameters you have used?

Thanks, Bjoern

Am 18.10.2014 um 14:33 schrieb Elizabeth Chia:

...

...

Hi there

I'm running into this error with cuffdiff:

...

I'm running galaxy locally on a cluster (1 head+3 compute nodes) with MySQL. Here's my hg summary:

...

Any clues?

I also keep getting the a similar 149 Internal Server error (with different Key Error) thrown when trying to install some tools. But strangely, after leaving it for awhile, it went back to normal. So I'm not too sure what's causing it.

Should I be updating galaxy to the latest stable one?

Please let me know if you require any other info.

Thanks!

liz

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/