You are running this on a local Galaxy?
And this step failed? https://galaxyproject.org/tutorials/var_hap/#left-aligning-indels
If so, did you index the genome for Samtools, Picard, and 2bit with Data Managers? Just indexing for BWA is not enough.
See this prior Q&A for the way to fully index a genome so that it works with all tools (BAM data in particular relies on the extra indexes listed out in the post): Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting - #2 by jennaj