dxfuse mounted filesystem is unstable
I wanted to bring up this issue again: https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/16019570466205-dxfuse-mounted-filesystem-eventually-fails-with-transport-endpoint-is-not-connected?page=1#community_comment_24253169694621. It doesn't seem my comment it triggering a notification.
I am mounting the dispensed imputed UKB genetic data in a cloud-workstation, but after 45mins of processing a .bgen file, I get a file read error, saying ‘Transport endpoint is not connected’, due to the dx-fuse mount breaking.
Simply remounting the directory is not an option as the progress made is lost. Is there a way to stop dx-fuse mounts breaking?
I am using the dxfuse-linux v1.4.0 release from GitHub.
Any advice is much appreciated. I know these mounts are not suppossed to be used for big tasks, but I have found they are more efficient than copying the data into the instance. When using the Rstudio app, I have no issue with the file mounts breaking, which is really useful, but the Rstudio app as other limitations.
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1 comment
Hi Oliver,
to contact DNAnexus technical support, please use the Help tab in the UKB-RAP gui, or the Support option on the UKB-RAP landing page, or email ukbiobank-support@dnanexus.com.
When the UKB-RAP was first set up, there was a community forum run by DNAnexus, but the current forum is monitored mainly by UKB staff. Any posts from before Dec 2023 were copied over from the old forum to this new one, but I don't think the notifications work.
If you get a resolution, please share the details here for other researchers.
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