I get the following error when using the GSEA software 'Enrichment Map Visualization' tool using the Cytoscape 3.7.1 application

Question

I am trying to visualize a GSEA analysis I conducted using the Broad Institute's GSEA Enrichment Map Visualization, however I get the following error and am not sure what the issue is: any help would be greatly appreciated.

INFO - successfully connected to cytoscape rest
INFO - successfully connected to cytoscape rest
INFO - Found enrichment map command
INFO - Get URL:http://localhost:1234/v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt
DEBUG - CookieSpec selected: default
DEBUG - Auth cache not set in the context
DEBUG - Connection request: [route: {}->http://localhost:1234][total kept alive: 0; route allocated: 0 of 2; total allocated: 0 of 20]
DEBUG - Connection leased: [id: 4][route: {}->http://localhost:1234][total kept alive: 0; route allocated: 1 of 2; total allocated: 1 of 20]
DEBUG - Opening connection {}->http://localhost:1234
DEBUG - Connecting to localhost/127.0.0.1:1234
DEBUG - Connection established 127.0.0.1:51968<->127.0.0.1:1234
DEBUG - Executing request GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1
DEBUG - Target auth state: UNCHALLENGED
DEBUG - Proxy auth state: UNCHALLENGED
DEBUG - http-outgoing-4 >> GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1
DEBUG - http-outgoing-4 >> Host: localhost:1234
DEBUG - http-outgoing-4 >> Connection: Keep-Alive
DEBUG - http-outgoing-4 >> User-Agent: Apache-HttpClient/4.5.2 (Java/1.8.0_201)
DEBUG - http-outgoing-4 >> Accept-Encoding: gzip,deflate
DEBUG - http-outgoing-4 >> "GET /v1/commands/enrichmentmap/gseabuild?edbdir=C%3A%5CUsers%5CHatim%5Cgsea_home%5Coutput%5Cmar15%5Cmy_analysis.Gsea.1552686798457%5Cedb&pvalue=0.005&qvalue=0.1&overlap=0.5&similaritymetric=OVERLAP&combinedconstant=0.5&expressionfile=C%3A%5CUsers%5CHatim%5CDesktop%5CJunior%5Csem+2%5CKarras+Lab%5CGSEA%5CKarrasEXP.gct.txt HTTP/1.1[\r][\n]"
DEBUG - http-outgoing-4 >> "Host: localhost:1234[\r][\n]"
DEBUG - http-outgoing-4 >> "Connection: Keep-Alive[\r][\n]"
DEBUG - http-outgoing-4 >> "User-Agent: Apache-HttpClient/4.5.2 (Java/1.8.0_201)[\r][\n]"
DEBUG - http-outgoing-4 >> "Accept-Encoding: gzip,deflate[\r][\n]"
DEBUG - http-outgoing-4 >> "[\r][\n]"
DEBUG - http-outgoing-4 << "HTTP/1.1 500 Internal Server Error[\r][\n]"
DEBUG - http-outgoing-4 << "Date: Sun, 17 Mar 2019 06:55:04 GMT[\r][\n]"
DEBUG - http-outgoing-4 << "Content-Type: text/plain[\r][\n]"
DEBUG - http-outgoing-4 << "Access-Control-Allow-Origin: *[\r][\n]"
DEBUG - http-outgoing-4 << "Access-Control-Allow-Headers: origin, content-type, accept, authorization[\r][\n]"
DEBUG - http-outgoing-4 << "Access-Control-Allow-Credentials: true[\r][\n]"
DEBUG - http-outgoing-4 << "Access-Control-Allow-Methods: GET, POST, PUT, DELETE, OPTIONS, HEAD[\r][\n]"
DEBUG - http-outgoing-4 << "Content-Length: 20[\r][\n]"
DEBUG - http-outgoing-4 << "Server: Jetty(9.4.10.v20180503)[\r][\n]"
DEBUG - http-outgoing-4 << "[\r][\n]"
DEBUG - http-outgoing-4 << "Failed: empty String"
DEBUG - http-outgoing-4 << HTTP/1.1 500 Internal Server Error
DEBUG - http-outgoing-4 << Date: Sun, 17 Mar 2019 06:55:04 GMT
DEBUG - http-outgoing-4 << Content-Type: text/plain
DEBUG - http-outgoing-4 << Access-Control-Allow-Origin: *
DEBUG - http-outgoing-4 << Access-Control-Allow-Headers: origin, content-type, accept, authorization
DEBUG - http-outgoing-4 << Access-Control-Allow-Credentials: true
DEBUG - http-outgoing-4 << Access-Control-Allow-Methods: GET, POST, PUT, DELETE, OPTIONS, HEAD
DEBUG - http-outgoing-4 << Content-Length: 20
DEBUG - http-outgoing-4 << Server: Jetty(9.4.10.v20180503)
DEBUG - Connection can be kept alive indefinitely
INFO - status:Internal Server Error
INFO - Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy{[Content-Type: text/plain,Content-Length: 20,Chunked: false]}
DEBUG - Connection manager is shutting down
DEBUG - http-outgoing-4: Close connection
DEBUG - Connection manager shut down

Answer 1

This is a tough one, because the only relevant lines from your GSEA debug log were these two:

DEBUG - http-outgoing-4 << "Failed: empty String"
DEBUG - http-outgoing-4 << HTTP/1.1 500 Internal Server Error

My recommendations to you at the time would've been

1. try closing all the programs, restarting them, possibly rebooting and restarting them, and even analyzing a completely different set of data to see if you get the same results, —or—
2. update to the latest Java 8, reinstall Cytoscape 3.7.whatever and the EnrichmentMap plugin from scratch, and re-download GSEA, —or—
3. lastly, try reinstalling everything on a completely different machine/OS and see if you get different results (e.g., try on a Mac or Linux if you had problems with Windows originally, or vice-versa)

I know that's lame, but sometimes that's how you solve weird computer errors, when the error message the application itself gives you is non-specific and unhelpful.

If you had seen the error message

None of the gene sets have passed the filter. Try relaxing the gene set filter parameters.

in the GSEA application logs, then you would've had the problem described in EnrichmentMap's GitHub issue #358, and the solution would be to use less stringent p- and FDR Q-value cutoffs, as prescribed in the "Tips on Parameter Choice" section of the EnrichmentMap documentation.

My problem was that GSEA's default cutoffs (p-value < 0.005 and FDR Q-value < 0.1) were entirely too stringent for my results set, and using the "Very permissive" settings of p-value < 0.05 and FDR < 0.25 from the documentation solved it for me.

Hopefully this benefits someone who ends up here after googling for "Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy," which is just a stupendously unhelpful error message when "None of the gene sets have passed the filter" is actually what went wrong. Maybe go thumbs-up this comment in the EnrichmentMap issue tracker, if you think the maintainers need to work on that.