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Question: Tophat run wont work
1
gravatar for michimaurin
3.6 years ago by
michimaurin • 20
michimaurin • 20 wrote:

HiI have been trying to run tophat for a while pretty much all day getting errors I would like to figure out if the problem is in my data or I am doing something wrong or it is actually an issue that is happening on the server.

 

Michelle 
tophat alignment • 1.4k views
ADD COMMENT • link •
modified 3.6 years ago by Martin Čech ♦♦ 4.9k • written 3.6 years ago by michimaurin • 20
1
gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello - The error messages tend to be specific. What is the error for your jobs? We can help decipher. Jen, Galaxy team
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Please give error message!

ADD REPLY • link written 3.6 years ago by Student-T • 0

I am also having errors with Tophat, except that no error message is produced. The run appears to start (turns yellow) and runs for a few hours but when I check on it the next day, it's somehow reverted back to gray and says "waiting to run"

I've never encountered an issue like this before and this has been repeated 3 times over the past few days. Should I try to upload my fastq files again and try again? When will the intermittent filesystem issues be resolved?

Thanks

 

ADD REPLY • link modified 3.6 years ago • written 3.6 years ago by jling • 70

Not sure how but it looks like the problem was resolved. Thanks.

ADD REPLY • link written 3.6 years ago by jling • 70

There were server issues during this time frame. Once confirmed, a banner was on Main explaining the problem. All that is now resolved. Very glad that you are able to proceed with your work now. Best, Jen, Galaxy team

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hi all, this is my first time using Galaxy, I think I am having the same problem. I submitted a file for Tophat, which appeared to start running, then the next morning reverted back to gray. I deleted and resubmitted last night, and this morning it turned back to grey again.

I should admit, these files are really large, one 17 GB and the other 19 GB. Could this be the problem? The message is "The job creating this dataset has been resubmitted."

Thanks!

ADD REPLY • link written 3.5 years ago by rtharak1 • 0

Hello - Please see Martin's reply. There were other issues going on at the time of the original question, but the description of your problem fits the cluster resubmission process. Thanks, Jen

ADD REPLY • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for Martin Čech
3.6 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Please see the responses in this thread: Tophat ends without error message

It is most probable that you are experiencing the same situation. (job is big = took too long = is being resubmitted to stronger machines)
ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by Martin Čech ♦♦ 4.9k
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