cBioPortal Datahub Public Dataset Load Into Database Issues

[Miu ki Yip]

Hi all,

I am trying to load some of the public data in the cBioPortal Data hub (https://github.com/cBioPortal/datahub/tree/master/public) into a local instance of cBioPortal but I am encountering errors loading the datasets in.

For instance, when trying to load the “msk_impact_50k_2026” study into the database, I am seeing the following errors in the stdout:



ERROR: data_clinical_sample.txt: line 5: column 20: Attribute name not in upper case.; value encountered: 'purity_estimate_from_mutations'

And 

ERROR: data_sv.txt: lines [25, 150, 154, (354 more)]: column 1: Sample ID not defined in clinical file; values encountered: ['P-0012686-T01-IM5', 'P-0013979-T01-IM5', 'P-0010429-T01-IM5', '(317 more)']

WARNING: data_sv.txt: lines [7423, 7840, 12522, (1 more)]: Hugo Symbol should not start with a number.; values encountered: ['48787', '30302_C.890', '1311DEL']

I am concerned that I am looking in an out of date location for the public datasets since a lot of the datasets in the GitHub repo linked have issues loading into the database.

Please let me know how I can get these datasets loaded or if there is an updated data repository.

Thank you!

[jagn...@gmail.com]

Hi Miu

thanks for reaching out to cBioPortal team. Which version of cBioPortal are you using for import?

The direct link to the study file is https://datahub.assets.cbioportal.org/msk_impact_50k_2026.tar.gz

You can obtain this from the main Study page on cbioportal.org. There is a download link for all studies right next to the Study title.

https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026

I will reach out to the data team since new studies sometimes have errors.


thanks
Jag