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uab-cgds-worthey / quac

🦆 Quality Control of WGS and exome samples 🦆
https://quac.readthedocs.io
GNU General Public License v3.0
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Obscure issue with Qualimap causing occasional failure #17

Closed ManavalanG closed 1 year ago

ManavalanG commented 3 years ago

Copied from: https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/sciops/pipelines/small_variant_caller_pipeline/-/issues/42

A fun one to be sure. Recently a few runs of the pipeline failed to run qualimap giving the following error

Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using 'localhost:37.0' as the value of the DISPLAY variable.

As background X11 is the GUI display engine used for linux displays, think the desktop or remote interfaces. A quick check and qualimap notes in their general information to unset the DISPLAY environment variable when using it on linux systems to prevent X11 issues when not using the tool with a display. The problem can easily be fixed using this recommendation from qualimap http://qualimap.conesalab.org/doc_html/faq.html#x11problem .

This isn't a consistent issue so my guess is that some combination of an X11 connection issue on a node for a specific user account running the pipeline caused X11 server access to be unreachable for a period of time and the issue reared it's ugly head.

Regardless, the fix is relatively easy and painless.

ManavalanG commented 3 years ago

mentioned in commit 93b240727c79d240cb92835bd111772a7efb1ac7

ManavalanG commented 3 years ago

mentioned in commit 28bbc54c9c2f8f38d23420886e4fb8105b09e1c3