We’ve found that there are different versions of Kallisto in our Docker vs. online server and the same index files will not work for both. We are in the process of updating all Kallisto versions to the latest 4.80 and rebuilding the index files. The timeline is ~1 week to update everything, but I can try provide the mouse index file to you earlier if you give me an email address.
We finished rebuilding the transcriptome index files with the latest kallisto version. Here is the link to the mouse transcriptome. I tested on my computer with the latest Docker image, and I was able to process an example dataset.
If there is a further erorr, there must be something specific with your data. Please let me know how it goes!