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files (which of course are now out of date) but not the new GO files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
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