Trinity assembly occuring but result coming empty..

Question: Trinity assembly occuring but result coming empty..

20 months ago by

Hello there, I am facing a serious issue now...for many days I am trying to denovo assemble my transcriptomes uaing Trinity. The problem occurring is that the job is completed with result showing "empty". Can anything be done to fix this problem. It will be very kind if you guys help me out here..

Thanks.

assembly trinity • 624 views

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modified 19 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by souradeep.galaxy • 10

19 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

When I have examined results in the past that came out this way, there was a problem with one of the following:

Input data too large and the job ran out of memory at the Trinity assembly site (external)
Inputs had some type of formatting problem, triggering a job failure (reasons can vary)
That same external site performing the Trinity assembly had some technical issues beyond the user's control
The host Galaxy server experienced connection issues with the external site (could be from either end - Galaxy or Trinity site)

For the first two, input changes are required. Read the help for Trinity. The tool in Galaxy is a wrapped version of the baseline tool (or rather, tools - all three are bundled in the wrapper).

For the last two, try rerunning. If repeated re-runs fail, then going back and checking for content-related reasons for the failure is the way forward. Should that not work, please send us a bug report: https://galaxyproject.org/issues/#usage-problem-reporting

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson ♦ 25k

19 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update:

Trinity was corrected again mid-day Friday 4/28/17 EST. Please re-run any jobs that failed. Issues with connections to the PSC Bridges server that executes these jobs has been unstable for a few weeks, but should be good now.

If you have jobs that were started after that time, that are still queued, will also need to be re-run (and the original grey jobs deleted/purged).

Sorry for the inconvenience, Jen, Galaxy team

ADD COMMENT • link written 19 months ago by Jennifer Hillman Jackson ♦ 25k

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