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.
> For example:
> 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.
> Elwood Linney
The wait is unfortunately due to two limits on large multicore jobs like
cuffmerge and tophat:
- 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
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 available nodes.
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
> 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
> 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:
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
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: