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ga4gh / ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
http://ga4gh.org
Apache License 2.0
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ga4gh-example-data/registry.db is malformed #1638

Open zhangb1 opened 6 years ago

zhangb1 commented 6 years ago

Hi ,

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

Database file 'ga4gh-example-data/registry.db' is malformed.
kozbo commented 6 years ago

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 commented 6 years ago

@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 commented 6 years ago

@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 commented 6 years ago

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 commented 6 years ago

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