Hi Delong, I used Tophat2 for 32 files and all worked well. I did not have any problem with it. Best wishes, Anto ________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Delong, Zhou [Delong.Zhou@USherbrooke.ca] Sent: 29 August 2013 14:57 To: galaxy-user@bx.psu.edu Subject: [galaxy-user] Tophat2 not working? Hello, I've been trying tophat 2 on the public server since last week but I don't get any results. I got one empty output for " the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error." one error with " Unable to queue job for execution. Resubmitting the job may succeed." and one empty output with no error message. It seems that tophat 2 is new on the server, has anyone run it with success yet? Thanks, Delong

Hello Delong, There were a small number of recent cluster errors during a short window earlier and it sounds as if you ran into that problem. Our apologies for the confusion. When this occurs, please just re-submit the job, as this is the best solution. Empty output indicates an issue with parameters (no hits). This would not result in an error. Reevaluating these would be advised - links to the full tool documentation are on the tool form itself plus help reminders. Take care, Jen Galaxy team On 8/29/13 5:57 AM, Delong, Zhou wrote:

Hello, I've been trying tophat 2 on the public server since last week but I don't get any results. I got one empty output for " the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error." one error with " Unable to queue job for execution. Resubmitting the job may succeed." and one empty output with no error message. It seems that tophat 2 is new on the server, has anyone run it with success yet? Thanks, Delong

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