Cytoscape - stringApp terms could not be mapped to any identifier

Question

[Jordan]

Hi,

I've been an avid user of Cytoscape for a little while and have recently been facing this problem of my gene terms not being recognized by the stringApp. I immediately see at the bottom "List of nodes that could not be mapped to any string identifier: [all terms I entered]" followed by the error "Your query returned no results"

I'm using Cytoscape 3.10.2 with Java 17.0.5. I've tried going back to Cytoscape 3.8 with Java 11.0.6, but stringApp fails to start for me in that version.

I've tried browsing the web for solutions but I haven't found step-by-step workarounds, and I'm wondering if anyone has any ideas.

Thank you!

[Scooter]

Can you post an example of your query that's failing? Also, what species are you working with?

[Jordan]

Attached are images of the query throwing the error, the task history, and the stringApp settings (using Homo sapiens). These proteins have been in past queries and both work on the string-db website. Thanks a lot for taking a look!

Answer 1

[Scooter]

OK, the key line is: "Unexpected error from server: PKIX path building failed". This indicates an SSL certificate issue -- for some reason, your computer is not accepting the certificate provided by either the string-db server or the Jensenlab server. I would suggest trying to upgrade to the latest Java, which should update $JAVA_HOME/lib/security/cacerts. That's the file that is the problem.

-- scooter

[Jordan]

I'll work to fix that, thanks very much!