Chai Fungtammasan DNAnexus Team
Comments
Recent activity by Chai Fungtammasan
-
If you want to go with WDL, using dx extract_dataset that Ondrej suggest might be a better solution. This way, you can have input as string. https://github.com/dnanexus/OpenBio/blob/master/dx-toolk...
- View comment
- 0 votes
-
I check with the support team and it seems that they have resolved it. One case is out-of-memory issue, while the other would need to change the configuration at the institution level.
- View comment
- 0 votes
-
In the monitor tab, you can "view log" for the job. Then there is a tracking of resource usage for every 10 mins. This checking method would not always work if there is a sudden surge of memory usa...
- View comment
- 0 votes
-
For the bug, it might be easier for support team to help with this since they could access your project. You can submit the ticket through the platform or send request to ukbiobank-support@dnanexu...
- View comment
- 0 votes
-
I forgot to note the fourth possible reason when the worker is dead due to out of memory. This might be something you could watch out.
- View comment
- 0 votes
-
I see. I got the wrong impression that you are only interested in subset of gene. The other thing you might do is to check in spark UI if the clusters are doing the job they suppose to do. I share ...
- View comment
- 0 votes
-
I usually lose connection from Jupyter in three occassions. 1) I was inactive for too long. Refresh browser, log in, and then it should work. 2) notebook timeout. You can see this in job log if you...
- View comment
- 0 votes
-
@UK Biobank DA Team?
- View comment
- 0 votes
-
The QC process are different because data were processed with different protocol. You may find this useful for WES data processing. https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-e...
- View comment
- 0 votes
-
If the native DNAnexus applet could have the ability to access database file, another solution is to use hybrid approach where the applet is native DNAnexus applet, but you chain them up as workflo...
- View comment
- 0 votes