The problem seems to be a genome that is no longer present. This could be due to a custom genome or Quickload being removed.

The line that fails is in the loadServers method within the BookmarkUnibrowControlServlet class. Within the session file attached by the user, the genome that is attempting to load is hg38+UCSC. This does not appear to be a default genome within IGB. When the session attempts to load the bookmark associated with the hg38+UCSC genome and cannot find the genome it leads to a null pointer.

To duplicate this issue, create a custom genome (see attached hg38 UCSC.fa). Load data (see attached data.bed) and save the session. Exit IGB. Start IGB and attempt to load the session. A null pointer will be thrown. Able to replicate on master (9.1.6) and on a previous release (9.0.2).

Possible changes: Could check for null pointers when attempting loadServers, however, the bookmark would still fail to load as the genome cannot be loaded. Would need to add new popup informing user that the bookmark contains a genome that is no longer available.

I will reach out to user to further investigate this issue.

Dear Dr. Konrad Grützmann,

I am investigating the issue regarding sessions failing to load in IGB. Thank you for including the session file as it allowed me to replicate the issue.

When I try to load the session on my computer IGB tries to load the genome hg38+UCSC. This appears to be a custom or Quickload genome, as it is not a default genome currently within IGB. Was this a genome you had added previously to IGB? Is this genome still available on your IGB machine?

Thank you,

Nowlan

If the hg38+UCSC genome is the same as the hg38 genome currently in IGB, you could add the attached personal synonyms in IGB and it will load the session. This page on the user's guide describes the synonyms.

To load a synonym file into IGB:

Select File > Preferences > Data Sources.
Under Personal Synonyms, select the file you want to add.
Select Version Synonyms to add synonyms.txt
Select Chromosome Synonyms to add chromosomes.txt
Choose and open file.
Restart IGB.
Note: If you clear your preferences or install a new version of IGB, you may need to reload your synonym files.

Can we close this now? Nowlan Freese

Have not heard back from user, so cannot confirm if the fix mentioned above worked for the user.

As the problem identified by the user is not new, closing issue for now.