Failed to conntact IGV configuration server when uploading genome from server

Question

[zengtony743]

I used IGV_2.3.23 under the linux... the tool is open but it said something like "can not connect with broad institute server" when I upload genome ... Is that because my IGV is old version or Broad Institute server has some issues?

Here is the information for the error :

GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://projects.gnome.org/gconf/ for information. (Details -  1: Failed to get connection to session: /bin/dbus-launch terminated abnormally without any error message)

[Pierre Lindenbaum]

"upload" ?! or fetch/download ? second case: are you working behind a proxy server ?

[zengtony743]

Since there is no reference genome on the "genome list "of IGV.. I need to upload genome to visualize my bam file (alignment file). Not quite sure about proxy server.. but I think I am not working behind a proxy server.

Answer 1

[GouthamAtla]

If you are uploading a genome from local machine, there is no need to worry about the error message. Whenever you launch IGV, it tries to connect to the server, which may fail due to any network issues, like proxy. You can ignore the connectivity issues as you have the genome fast a file.

But it seems to be a Linux issue rather than IGV. It's permissions issue. If you are trying to launch IGV from different users account and if you don't have necessary permissions on dirs which IGV is using, like /tmp, causes this error to pop up.