Ondrej Klempir DNAnexus Team
Comments
Recent activity by Ondrej Klempir
-
Awesome! thanks
- View comment
- 0 votes
-
I would suggest working with pVCF using Hail: https://github.com/dnanexus/OpenBio/tree/master/hail_tutorialhttps://documentation.dnanexus.com/science/using-hail-to-analyze-genomic-data Alternativel...
- View comment
- 0 votes
-
Could it be related to https://github.com/dnanexus/dxfuse?tab=readme-ov-file#common-problems? Could you make sure that the project is mounted? I have no idea why and when to use dx-mount-all-input...
- View comment
- 0 votes
-
Yes, you did the same installation things/steps I would do as well. I do not have any working example ready now, just sharing my thoughts about this. What I would try to do next would be to make su...
- View comment
- 0 votes
-
Github page is here: https://github.com/dnanexus/dxfuse, you can test it and later install it from there. You can create an asset using Makefile: https://documentation.dnanexus.com/developer/apps/d...
- View comment
- 0 votes
-
From what I am reading and since you have developed your custom dnanexus app(let), I am wondering whether you also added dxfuse as a prerequisite/installation to your applet? My understanding is t...
- View comment
- 0 votes
-
You may try to set up the workspace and project context inside your applet, as it is described here:https://documentation.dnanexus.com/developer/cloud-workstations/cloud-workstation#step-3-setting-...
- View comment
- 0 votes
-
if the issue persists, feel free to forward it to DNAnexus technical support team: ukbiobank-support@dnanexus.com. They will be able to check the particular job and job log.
- View comment
- 0 votes
-
Is the job eventually finish with failed status? It seems to me still like an issue with memory? Regarding the file size, have you tried first testing the indexing on a smaller file? e.g. just subs...
- View comment
- 0 votes
-
For running Hail, I would use instance type with a lot more memory and also ssd instead of hdd.
- View comment
- 0 votes