computeMatrix with errors Mean of empty slice

[ShuZhang0917]

Dear deepTools group,

Thanks for your wonderful tool. I used deeptools 3.5.1 and Python 3.9.12.

When I was running computeMatrix for ATAC-seq peaks using code: computeMatrix reference-point
-S ESC_ATAC.bw
-R mm10_genecodeVM23.bed
--referencePoint TSS
-a 1000 -b 1000
-out matrix_Genes_ES_bulk.tab.gz
--outFileSortedRegions ES_bulk_region_order.bed

I got errors with thousands Skipping lines: Skipping ENSMUST00000178569.1, due to being absent in the computeMatrix output. /software/miniconda3/lib/python3.9/site-packages/deeptools/heatmapper.py:1219: RuntimeWarning:

Mean of empty slice

After that, results of plotHeatmap was empty.

Could you please give me some advice? Thank you so much!