Hello Colleen,
This helps to localize the problem to the new GO files you are working
with (the software did not change).
A small sample of your original data, run against the old and new GO
files until completed, then compared to eachother, is probably the best
way to understand what it is about the new files that is
different/causing all of the new joins. This may help you to find a data
problem, or to understand why the change is present (if it is a correct
change).
Good luck with your project,
Jen
Galaxy team
On 4/25/13 7:06 AM, Colleen Burge wrote:
Hi Jen,
I've been using this tool to join based on one key, and never had any
trouble. I've tried with my old data sets and the new GO files, and
once again they don't ever finish--I stopped it after 12 hours.
I'm wondering if there's also an issue with my account?
Thanks,
Colleen:)
On Tue, Apr 23, 2013 at 4:35 PM, Jennifer Jackson <[email protected]
<mailto:[email protected]>> wrote:
Hello Colleen,
The tool " Join two Datasets" could potentially create a very
large dataset if the inputs shared enough common keys. The
pathological case where every input from the new query was joined
with all of the entries in the target would lead to longer
processing times (and potentially memory problems), if either of
these were large to begin with. The results in this case most
likely wouldn't be useful, so even if the job is eventually
successful, you will want to investigate the content.
I would suggest one more test: taking one of your old datasets,
and using it as query against the new GO files, then comparing the
results vs those you had from the old GO files (or generate it
again, new, as a direct comparison). I job that runs longer should
be left to just execute. If it fails (likely a memory problem),
then consider only running a sample of the data in this manor.
This will probably tell you much about the composition of the new
GO files themselves and potentially how to correct the problem. If
the new GO files do not seem to be the problem, then you will know
that the issue must be in the new data - perhaps something went
wrong in the annotation process that is linking in too many
assignments?
Please let us know how it goes and if you need more help,
Jen
Galaxy team
On 4/23/13 1:04 PM, Colleen Burge wrote:
Hello all,
I've been using the "Join, Subtract and Group" to join my
transcriptome/annotation data to GO and GO Slim for some time (in
the Main galaxy). I just updated my GO files as I've run a a new
data set, and have been having trouble with the joining function,
it never seems to complete (while before it would be done in just
a few minutes). It works just fine joining my "new data" with my
"old" GO files (which of course are now out of date) but not the
new GO files from both my collaborator and from EBI (specifically
the unipro). Not sure if its a file size limitation?
Thanks,
Colleen
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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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