The kmer.annotate.cits.sh script usage information states:
# The script requires two input arguments:
# 1.) the bed file of truncations to work on
# 2.) the fasta file of the genome used for alignment. This fasta file needs to be indexed with a "genome.fasta.fai" index file in the same directory.
# Example usage: kmer.annotate.cits.sh my.truncations.bed genomes/genome.fasta
The kmer.annotate.cits.sh script usage information states:
However, there are locations in the script (e.g., https://github.com/jaffreylab/miCLIP_MiMB_2016/blob/master/kmer.annotate.cits.sh#L15 , https://github.com/jaffreylab/miCLIP_MiMB_2016/blob/master/kmer.annotate.cits.sh#L19 ) at which the script ignores the input genome information and instead attempts to access a hard-coded path: /home/shareowner/genomes/human/all_chrom.fa . As one might imagine, this causes errors.