Could you let me know what is in the "... and so on ..." bit of the error message as that will help us diagnose what exactly went wrong.

It's possible you are running into an issue where if data on your disk has been corrupted or if you have manually tried editing the contents of your Geneious data directory Geneious can fail to startup like you describe. If that is the cause, then you can delete a file called ".localDatabase/index.txt" in your Geneious data directory and try starting Geneious again. Geneious will start up a bit slower while it recreates the index.txt file, but hopefully it should work. For example for me I would delete the file called

/Users/matt/Geneious 5.0 Data/.localDatabase/index.txt

Hello

I deleted that file and it seems to be working again. Thanks!

Hello

Unfortunately, I still have not been able to restore my Geneious data. The program opens now and displays icons for all of the documents, but when I actually try to open a document I now get the error message:

User Message:
Failed to load document contents of AF006434 PAU

For document AF006434 PAU in LocalDocuments/Incoming/Caracal NADH, Can't find document data (ID=.1273876949803.80) in folder /Volumes/GENEIOUS 2/Geneious 5.0 Data 2/.localDatabase/data/originalDocuments. If you have copied your data from another location, make sure you copied the entire 'Geneious 5.0 Data 2' folder



Details:
Document Location: /Volumes/GENEIOUS 2/Geneious 5.0 Data 2/.localDatabase/data/projects/Incoming/Caracal NADH/urn_3alocal_3akathryn_3a1273876949801.2092.1273876949830.81.ref4.xml and /Volumes/GENEIOUS 2/Geneious 5.0 Data 2unknown id .1273876949803.80

Stacktrace:
java.io.IOException: For document AF006434 PAU in LocalDocuments/Incoming/Caracal NADH, Can't find document data (ID=.1273876949803.80) in folder /Volumes/GENEIOUS 2/Geneious 5.0 Data 2/.localDatabase/data/originalDocuments. If you have copied your data from another location, make sure you copied the entire 'Geneious 5.0 Data 2' foldercom.biomatters.core.documents.DocumentLoadException: java.io.IOException: For document AF006434 PAU in LocalDocuments/Incoming/Caracal NADH, Can't find document data (ID=.1273876949803.80) in folder /Volumes/GENEIOUS 2/Geneious 5.0 Data 2/.localDatabase/data/originalDocuments. If you have copied your data from another location, make sure you copied the entire 'Geneious 5.0 Data 2' folder
at com.biomatters.core.documents.AnnotatedDocumentImplementation.getInternalDocumentElement(AnnotatedDocumentImplementation.java:1890)
at com.biomatters.core.documents.AnnotatedDocumentImplementation.getProxyInternalDocument(AnnotatedDocumentImplementation.java:914)
at com.biomatters.core.documents.AnnotatedDocumentImplementation.getInternalDocument(AnnotatedDocumentImplementation.java:789)
at com.biomatters.core.documents.AnnotatedDocumentImplementation.getDocumentOrThrow(AnnotatedDocumentImplementation.java:776)
at com.biomatters.geneious.common.documents.DocumentCache.loadInternalDocuments(DocumentCache.java:95)
at com.biomatters.iseek.gui.ViewersPanel$6.run(ViewersPanel.java:335)
at java.lang.Thread.run(Thread.java:637)
Caused by: java.io.IOException: For document AF006434 PAU in LocalDocuments/Incoming/Caracal NADH, Can't find document data (ID=.1273876949803.80) in folder /Volumes/GENEIOUS 2/Geneious 5.0 Data 2/.localDatabase/data/originalDocuments. If you have copied your data from another location, make sure you copied the entire 'Geneious 5.0 Data 2' folder
at com.biomatters.plugins.local.v.getElement(DirectoryRepository.java:2285)
at com.biomatters.core.documents.AnnotatedDocumentImplementation.getInternalDocumentElement(AnnotatedDocumentImplementation.java:1888)
... 6 more

For anyone else reading this, I've also been corresponding with Kathryn by email. Her data is all stored on a USB drive and it turned out an entire folder of non-critical data inside the Geneious data directory on the USB drive went missing which lead to the original error. This new error indicates that more files seem to be missing. If every document is giving this error that indicates that the entire folder that stores all the actual data inside every document is also missing from your USB drive. When you first start up Geneious it just loads a small summary of your documents so you can see what they are but the actual data is stored in different files.

When you copied your data to the USB drive did you copy the entire "Geneious 5.0 Data" folder? We've had people before browse around inside their "Geneious 5.0 Data" folder just copying the files they think they need, leading to this problem which is why we recommend copying the entire folder.

If you did indeed copy the entire folder then it sounds like your USB drive is faulty and loosing files. In that case, unfortunately the only thing I think you can do to is to revert to your most recent backup of your data. If you don't have a backup then you could zip up your entire Geneious data directory and email it to me and I can see if there is any recoverable data there, but it sounds unlikely given the error message.

Hi Shane

I was afraid that the USB drive had been corrupted beyond repair since these problems started out of the blue. I have retrieved my data from a backup folder that I had on a desktop computer and will buy a more substantial external hard drive to store the data today. Thanks for your help.

Even if you're storing your data on a portable drive, you should still use File->Export->All Local Documents... to make an archive of the data which you can store on another drive and can be imported into Geneious if your portable drive gets corrupt. It is simple good practice to have multiple copies of your data on multiple drives.

Shane