On Oct 18, 2013, at 12:48 PM, Elwood Linney wrote:
My histories seem to be stopping their processing around the
Tophat-cuffmerge steps since the change over of Galaxy online. Sometimes a red box appears
over my history name but disappears in a minute or less.
I am wondering, given the way the Toolshed now looks different for RNAseq work, if some
changes have been made that are disallowing the procedures I used previously.
I run larger Fastq files (100 million to 200 million 50bp single-ended reads per sample).
I have been grooming my illumina fastq's, using Tophat (not Tophat2) for alignment,
then Cuffmerge, then Cuffdiff. This worked in the past but my history are just getting
thru Tophat or Cuffmerge and stalling. Should I be doing this in a different manner?
This has been my second time around with these datasets after it was suggested that I
delete and start all over again.
The wait is unfortunately due to two limits on large multicore jobs like cuffmerge and
- Only 1 job per user could previously be placed into the cluster queue for multicore
jobs - as of this morning we've increased it to 2
- All of the nodes available for running multicore jobs are currently allocated, so
there is some wait, even once your job is allowed to be added to the queue
You had a tophat job running prior to increasing the limit to 2, so no other jobs would
have even been eligible to complete until that job finished. After the increase you still
have the same tophat job running but another one has been queued, and it is waiting for
I hope you'll find that the wait time for these is shorter than on the old Galaxy
Main. We are also expecting to add additional hardware to this pool soon.
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: