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
Hi Elwood,
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 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 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 soon.
--nate
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