pipeline failed when using references.wdl

[cmf1997]

hello there,
wonderful pipeline for all the tools
I was trying to process dnase data from fastq
and I was conducting make reference json for specific genome and read length because I did not see any template for any genome
there is the Cromwell.out and std.err std.out
cromwell.out.txt
30422604.out.txt

30422604.err.txt

obviously, there was a error created when running "build_bowtie_index"

"Warning: Encountered reference sequence with only gaps"

how can I fix this issue and is there any problem I should take care of ?
any suggestions would much appreciated!