Error with exomiser 13.2.1 Caused by: org.h2.jdbc.JdbcSQLNonTransientConnectionException:

[fionaelisa]

Hi, I have been using Exomiser 12.1.0 for over a year without any problems, but I am having trouble getting Exomiser 13.2.1 up and running, and it seems to be a problem with the h2 db?

All the error codes say something like:

org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/2302_hg38/2302_hg38_genome;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200]

Caused by: org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database URL "jdbc:h2:file:data/2302_phenotype/2302_phenotype;SCHEMA=exomiser;MODE=PostgreSQL;IFEXISTS=TRUE;AUTO_RECONNECT=TRUE;ACCESS_MODE_DATA=r;". Use an absolute path, ~/name, ./name, or the baseDir setting instead. [90011-200]

Hope you can help - thanks!

[julesjacobsen]

Have you checked that your exomiser.data-directory is pointing to an absolute path? The error message is complaining that your path data/2302_hg38/2302_hg38_genome is a relative directory.

If so, can you provide your application.properties

[julesjacobsen]

Did you try exomiser.data-directory=C:\\Users\\username\\exomiser-cli-13.2.1\\data?

[fionaelisa]

Yes, I tried changing to an absolute path but it came up with same errors. This is my application.properties. I also tried with exomiser.data-directory=C:\Users\username\exomiser-cli-13.2.1\data and other paths.

[julesjacobsen]

No, exactly that, with the \\ path.

[julesjacobsen]

Alternatively exomiser.data-directory=C:/Users/username/exomiser-cli-13.2.1/data might work. Sorry, I don't have a Windows machine to test this on.

[fionaelisa]

Thanks so much! The second option has worked!

[julesjacobsen]

Awesome!