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Question: Unicycler genome assembly failure
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gravatar for renae.geier
14 months ago by
renae.geier • 40
Milwaukee, WI
renae.geier • 40 wrote:

Hi all,

I have some Illumina reads and Nanopore reads I'd like to assemble using Unicycler. I uploaded the raw fastq files, groomed them, and ran Unicycler on these with the default settings. I received the following error: "Remote job server indicated a problem running or monitoring this job." Does this sound like a Galaxy problem or a problem that I can solve? Any help is greatly appreciated! Our Linux computer is not connected to the internet so I'm having trouble getting programs installed there and I'm stuck with a Windows for the time being, but alternative assembly methods are also greatly appreciated!

Thanks! Renae
assembly unicycler galaxy • 683 views
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modified 14 months ago • written 14 months ago by renae.geier • 40
1
gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi Renae,

This is the same answer as I sent you directly, but for others that encounter the issue, this is the status:

The Unicycler tool has known issues. All jobs will result in a server error.

This is a priority fix occurring right now. Please follow the linked ticket for progress on the correction. We'll update as the changes are implemented and all tests pass: https://github.com/galaxyproject/galaxy/issues/4516

Thanks again for reporting the issue! Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for renae.geier
14 months ago by
renae.geier • 40
Milwaukee, WI
renae.geier • 40 wrote:

Hi Jennifer,

My assembly with Unicycler completed today and seems to be working well!!

Thanks so much!!
ADD COMMENT • link written 14 months ago by renae.geier • 40

Thanks for writing back. This was a priority fix and our testing is still in progress. I'll update the ticket once all checks pass.

ADD REPLY • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
1

All tests pass and the tool is ready to use. We made a few more corrections and closed out the ticket I linked. Thanks!

ADD REPLY • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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