Why is my indexer continually running?

Geneious Prime uses the Lucene indexer as the basis of the searching function. When the indexer is running, you will see an “Updating Search Index” indicator underneath the Sources panel to the bottom left of the Geneious window.  The indexer can get stuck on certain really large documents, or if you have documents in your database which are corrupted. If you hover your mouse over the indexing indicator, it will identify the document that is causing the problem in a tool tip. Delete that document (export it to a safe place if you want to keep it) and then restart Geneious and the indexer should finish.

You can also pause the indexer by clicking on the indexing indicator.  This may take pressure off the hard drive and enable other tasks to finish.  Don’t forget to restart the indexer as features such as enzyme lists, or the Test with Saved Primers operation will not function correctly when the indexer is paused.  


indexing.png      indexing_paused.png


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  • Avatar
    Lizbeth Sayavedra

    Hi! I am having this problem since a while and Geneious is running incredibly slow. I tried to find the files that are causing the problem, but even if I move my mouse over the legend of "updating search index: 283893 items" it does not say which files are causing the problem. Is there another way to know where are the conflicting files?



  • Avatar
    Helen Shearman

    Hi Lizbeth,

    Is this number slowly decreasing?  Or does the indexer appear stuck at 283893 items?

    How much RAM is available on your computer and how much RAM do you currently have allocated to Geneious?  In the memory usage bar, does Geneious appear to be using all of the available memory?  The memory usage bar will appear in the bottom left hand corner of Geneious.  To turn the memory usage bar on, go to Tools -> Preferences -> Appearance and Behaviour and tick the box next to "Show memory usage bar".

    Kind regards,


  • Avatar
    Hilary Miller

    Also make sure you've erased all your deleted items as if you have lots of documents in there that can really slow things down

  • Avatar
    Lizbeth Sayavedra

    Thanks, after 10 hours erasing the deleted items, it finally has normal speed.