Ok, that explains the problem.
The genome is in a list, with some basic data, but hasn’t been fully indexed on your server.
When working with BAM data, the Samtools index is important. Some tools also use the Picard and 2bit.
If you instead want to continue using the genome as a “custom genome” fasta from the history, you’ll need to 1) make sure the formatting is cleaned up 2) promote the genome to a “custom build”, then assign that database to your data. Some tools require a database is assigned – either natively indexed by a Data Manager, or indexed just in your account as a Custom Build.
Warning: using a custom genome or build takes up much more resources, every time you run a tool. Using data managers to index the genome will make jobs run much faster.
When there are custom genome problems, problems tend to not show up during mapping, but with later steps. The fasta format is very important, or expect more problems. This may mean that you will need to remap.
The first FAQ covers the details and the second explains how to avoid even more problems when incorporating reference annotation (if you decide to do that). In short, whatever chromosome identifier(s) you decide to use in your genome, it must be an exact match for the chromosome identifier(s) in other inputs.