ga4gh-example-data/registry.db is malformed

[zhangb1]

Hi ,

When I ran the the command ga4gh_server , it came out the error

Database file 'ga4gh-example-data/registry.db' is malformed.

[kozbo]

I need more information to help you. Are you trying to run the demo?

That error generally means that the registry.db is out of sync with the version expected by the server. The usual process to fix this problem is to delete the db and build a new one.

[zhangb1]

@kozbo Thank you for your replay.

Yes, I want to run the demo. but seems the example file registry.db for downloading is malformed.

Do you have the new example for the test run?

[rdeborja]

@zhangb1 we ran into the same issue and rebuilt the database using the ga4gh_repo command (http://ga4gh-server.readthedocs.io/en/stable/datarepo.html).

[jonejkim]

We have encountered the same malformed database problem few weeks ago, but we could no longer replicate that problem today when ga4gh-server is built and ran on from the dockerfile in this repository.

However it is still possible to replicate the problem if we were run the server based on instructions in http://ga4gh-server.readthedocs.io/en/latest/demo.html , and the example data linked (https://github.com/ga4gh/ga4gh-server/releases/download/data/ga4gh-example-data_4.6.tar) there.

[hannah413]

I am also getting this error while working through the demo.