[go: nahoru, domu]
Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Error with exomiser 13.2.1 Caused by: org.h2.jdbc.JdbcSQLNonTransientConnectionException: #516

Closed
fionaelisa opened this issue Sep 11, 2023 · 7 comments
Closed

Error with exomiser 13.2.1 Caused by: org.h2.jdbc.JdbcSQLNonTransientConnectionException: #516

fionaelisa opened this issue Sep 11, 2023 · 7 comments

Comments

@fionaelisa
Copy link

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
Copy link
Contributor

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
Copy link
Contributor

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

@fionaelisa
Copy link
Author

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
Copy link
Contributor

No, exactly that, with the \\ path.

@julesjacobsen
Copy link
Contributor

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
Copy link
Author

Thanks so much! The second option has worked!

@julesjacobsen
Copy link
Contributor

Awesome!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@julesjacobsen @fionaelisa