IGV load error when trying to view vcf file

Question: IGV load error when trying to view vcf file

2.8 years ago by

Belgium

Hi,

I'm trying to view a vcf file that was generated on our local galaxy server (tracking master of ubuntu 14.04.3) in a local igv. When I click the "local" link IGV reports the following error:

Error loading http://redacted/display_application/687964d2abc1d496/igv_vcf/local_default/4e36def3785e7031/data/galaxy_687964d2abc1d496.vcf.gz: Unable to create BasicFeatureReader using feature file , for input source: http://redacted/display_application/687964d2abc1d496/igv_vcf/local_default/4e36def3785e7031/data/galaxy_687964d2abc1d496.vcf.gz

The igv jar was already running before I clicked the link.

Thanks for the help!

16.01 igv galaxy • 1.1k views

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modified 2.8 years ago • written 2.8 years ago by matthias.desmet • 150

2.8 years ago by

matthias.desmet • 150

Belgium

matthias.desmet • 150 wrote:

Follow up:

Fixed the issue, apparently there was something wrong in the nginx configuration. Default value for proxy_max_temp_file_size was set to 1024 MB, which caused the large file downloads to fail.

tl;dr
When using x_accel_redirect, make sure the proxy_max_temp_file_size value is set to a large enough value.

ADD COMMENT • link written 2.8 years ago by matthias.desmet • 150

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool path does not match up with the master branch. See http://getgalaxy.org for more details about how to keep your local current.

The local IGV browser does need to be fully launched before using this function, but I don't think that is the root problem for your situation.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thanks for you time. Could you clarify what you mean with the tool path doensn't match up? I'm not really sure what you mean. Our code is fully up to date with the master branch of the Galaxy repo. Could that be the issue? Should I track a specific branch?

Thanks!

Matthias

ADD REPLY • link written 2.8 years ago by matthias.desmet • 150

Hi,

Just some follow up, so far no succes.

We've updated our Galaxy to the most recent release, so we're now tracking the 16.01 branch. While trying to debug, I copied the url in the error in a browser window, which resulted in a download of the correct file.
Could this be an IGV related issue? I'm using IGV 2.3.68.

When I try to recreate the issue on use galaxy.org, I get a unrelated error, because the job to create a tabix index fails.

Got any more ideas?

Thanks!
Matthias

ADD REPLY • link written 2.8 years ago by matthias.desmet • 150

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