Warning! No unique k-mers for k24

[Delva Leão]

Dear Mehran,

I manage to get ubismap for my Dasypus novemcinctus genome going! 

However, I'm running into this issue when on the merge bowtie outputs step.

For ~/scratch60/dasNov3.0_973_genomeMappability/umap/kmers/k24/JH563979.1.k24.uint8.unique.gz found 0 unique regions
Warning! No unique k-mers for ~/scratch60/dasNov3.0_973_genomeMappability/umap/kmers/k24/JH563979.1.k24.uint8.unique.gz
This could occur if the order of chromosomes in the chrsize.tsv file does not match with the provided genome.fa file
Saved ~/scratch60/dasNov3.0_973_genomeMappability/umap/kmers/k24/JH563979.1.k24.uint8.unique.gz
Exiting successfully.

My chrsize.tsv and genome.fa have the same order, but my genome is edited down to 973 scaffolds because the whole genome is huge (45K scaffolds) and somewhat fragmented.

How worried should I be about this? Can I move forward with creating the mappability file? Ultimately, I'm creating this mappability file to serve as one of the inputs for the MosaicForecast tool.

I appreciate your input,

Delva