Infinite Tophat Run

Question: Infinite Tophat Run

6.2 years ago by

I am running Galaxy online, excuting TopHat on a fastq file, something which I previously have done without problems. This time, my data file is maybe double the size and does not seem to ever get done (I'm on the fourth day or so). Previously I have never experienced that this has taken more than 24 hrs. Any idea what could be going on? /Philip

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modified 6.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.2 years ago by Jonsson, Philip • 10

6.1 years ago by

David PANG • 20

United States

David PANG • 20 wrote:

Hi, there, I just got two genome-wide Bisulfite sequences from BGI and start to analyze the data. I am trying to use Galaxy; but I find there is no such platform available. Does anybody know where I can find this kind platform at Galaxy or other places. Thanks David -- David PANG, Ph.D. Department of Plant and Soil Science, Texas Tech University Lubbock, TX 79409 Work: 806-742-5073(ext.263) FAX: 512-582-8568 Cell: 512-850-9169 Website https://cottonpang.wikispaces.com/

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6.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Philip, I'll reply to your bug report, but just for general information to others, the most common cause for delays is that the Galaxy main server is busy and/or the job itself large. Jobs can be queued ('grey') for up to a day when we are at peak usage. It is important to not stop/restart jobs at this stage, otherwise they move to the end of the queue again. Once running ('yellow'), a job such as Tophat has normally up to 72 hours to complete. How long a job will run depends on the type of job, the parameters used, and the size of the inputs. Should there be a job size issue, the job will error out, often indicating that it is too large to run on the public Main instance (and sometimes any instance) due to the parameters selected and the inputs. In these cases, the next step is reviewing the parameters and inputs, making adjustments, and then determining if a cloud solution with more resource (often memory) is a potential solution worth testing out. If jobs are urgent, a cloud or local solution is also an option, large or small. Which to choose depends on what resource you prefer or have access to: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices http://usegalaxy.org/cloud http://getgalaxy.org Occasionally there are other factors. Please feel free to write in, as you have done, with a bug report to check in and see if this is the case. http://wiki.g2.bx.psu.edu/Support#Reporting_tool_errors Good question and I will be getting back to you shortly about your specific situation, Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

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