ClueGO: not able to update KEGG pathway database

[sandy...@gmail.com]

Hi,

I got an error when updating the KEGG pathway data in ClueGO - it is related to http://rest.kegg.jp/get/hsa04933 which caused the updating process to terminate. Any clue to resolve this?

Thank you!

Best regards,

Sandy

[Bernhard]

Hi Sandy, could you give us more details? Perhaps run ClueGO from a terminal and send us the output when it happens. We tried to update KEGG for human and it works.

Best

[sandy...@gmail.com]

Hi Bernhard,

Thanks so much for following up. I was running ClueGo as cytoscape plugin, and on choosing the "Update Ontologies" & "KEGG - Update KEGG Pathways", this error message popped up:

"Internet connection seems to be interrupted or the link has changed: Server returned HTTP response code: 403 for URL: http://rest.kegg.jp/get/hsa04810. Check in the *.properties file in the /your_home_folder/ClueGOSourceFiles/Homo Sapiens/ folder!"

The problem is definitely not due to internet connection, but the "Homo Sapiens_KEGG_Pathways_[download date].txt.gz" file downloaded to the folder in the error message is incomplete - extracting the file gives the error "unexpected end of data". I guess there is probably problem with http://rest.kegg.jp/get/hsa04810 that caused the download termination?

Thank you very much!

Best regards,

Sandy

[Bernhard]

Hi Sandy, the link seems to work now. Probably it was just a maintenance of KEGG but it is working again. Did you try to update again, and do you still get the error?

Best

[Sandy Lam]

Hi Bernhard,

I just tried with my laptop (previously with PC), the problem persists. But an interesting observation was that, the % of download completed at the moment the error message popped up varied in different update attempts (e.g. 61%, 72%, 76%), and so did the URL showed by the error message (e.g. http://rest.kegg.jp/get/hsa04721, 04975...). Would it be that the error message was due to some time limit in downloading the pathway file?

The update I chose in the pull-down box is "KEGG - update KEGG pathways".

Thank you!

Sandy

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.
To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/66f43e6c-4394-4334-b049-1638a99d2f4a%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.