I refer to bwa.kit version downloaded on 17Feb2017 using this link:

https://downloads.sourceforge.net/project/bio-bwa/bwakit/bwakit-0.7.15_x64-linux.tar.bz2

It seems that this version of bwa.kit contains an obsolete URL for GRCh38 download in run-gen-ref file.

It seems that the current URL for GRCh38 should be:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz

See URL change notice here:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/README_change_notice.txt

Could you check and correct, if necessary?
Thank you,
Alexey