LiftoverVcf Encountered a contig, chr15 that is not part of the target reference.
I try to run modified for my trait and cohort of interest tutorial GWAS study from here:
and on array data liftover step, which I perform using this reference:
https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=1000
as suggested in here:
https://github.com/dnanexus-rnd/liftover_plink_beds
as from whatever reason the folder "Bulk/Exome sequences/" lacks subdirectories “Exome OQFE CRAM files/helper_files/" containing required "GRCh38_full_analysis_set_plus_decoy_hla.fa”
I encounter an error as specified in the headline, which I don't know how to handle. I'm new to GWAS and cloud computing, so please don't assume any prior knowledge or understanding on my side. I'd be very grateful for any help.
Comments
3 comments
Hi Bartosz,
the file should be present in your project. It is present in my project, see image.
If your project is quite old, you might need to dispense a new project, or refresh the old project.
See these articles for more information.
https://community.ukbiobank.ac.uk/hc/en-gb/articles/26343840019485-How-to-update-dispensed-data
https://community.ukbiobank.ac.uk/hc/en-gb/articles/15961013126429-Why-is-data-missing-from-my-UKB-RAP-project
Note that it is possible to copy any code or derived results from one project to another using the
dx copycommand in the dx toolkit.Thank you for using the forum.
Hi! I don’t think my project is old, since I created and dispensed it just 2 months ago. I don’t see the “Exome OQFE CRAM files” folder, there’s something else instead. How often should I update the project folder? At the moment, both “Check for updates” and “Dispense more data” are inactive, with a note saying it’s due to high demand.
Hi Ilakya,
Firstly, please check whether “Exome OQFE CRAM Files” is a subfolder within “Exome Sequences”.
Refresh and Re-Dispense are not currently possible for any projects, probably for the whole of this week, see the DNAnexus Status page here https://status.dnanexus.com/ . I suggest you “subscribe to updates” to be notified when this is finished.
In general, researchers are likely to want to refresh their projects after the UKB-RAP Main Copy of the data has been updated with new data. The previous update to the Main Copy was in March 2025, see https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/data-structure/data-release-versions , and the next update to the Main Copy is likely to be late 2025, see the future releases article https://community.ukbiobank.ac.uk/hc/en-gb/articles/26655455734301-Upcoming-data-release-v20 . Some researchers might refresh their projects in order to remove withdrawn participants. Other researchers prefer to remove withdrawn participants manually.
I don't think you need to refresh your project. I suspect you might need to dispense an additional bundle of data to your current project. If your current project is less than 5 PiB, then you don't yet have the individual-level data for the Whole Exome Sequences or the Whole Genome Sequences. The full data is around 26 PiB.
Only projects that are Tier 3 (or Student or LMIC) in AMS can dispense the WES and WGS data. Only people with Administrator permissions for the specific UKB-RAP project can dispense additional bundles. See https://community.ukbiobank.ac.uk/hc/en-gb/articles/15961013126429-Why-is-data-missing-from-my-UKB-RAP-project . If this is the issue, then I think you will need to wait for the scheduled maintenance to finish.
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