Hi @Isa
Fasta files have a specific format. This is an older FAQ but still has useful details. There are many other references for the format online too.
→ Datatypes - Galaxy Community Hub
To use a fasta file as a reference target, you can use it directly from the history just like the other inputs. This is named a “custom genome” in Galaxy (but could also be a transcriptome or exome). If you need a database metadata key, you can create one for your custom genome, and that is called a “custom build”. You’ll be able to assign that to datasets, and some tools will interpret it.
→ FAQ: How to use Custom Reference Genomes?
For this part
The fasta you posted doesn’t seem to have a >identifier title line at the start. But maybe that was excluded from the copy/paste? Be sure to review those lines when you are confirming the file format against the guide above.
For this error
the tool is probably expecting a database assigned to the input dataset. If this was from Freebayes: that tool does require an assigned database. Your input either didn’t have a database assigned, or had the wrong database (that didn’t include a sequence with that identifier). When you create a custom build, that is what creates a fasta index for your custom genome. Then the assignment of that custom build is what links the fasta index to your dataset.
Maybe I am overexplaining or maybe I missed something… but if you have followup questions, please ask 
We’d also be interested in knowing if you solve this!