Hello,
I’m getting an error when attempting to use the Deeptools python package. I used this as recently as yesterday with no issues. Now the tool “plotHeatmap” is returning this error: site-“packages/deeptools/heatmapper.py:1219: RuntimeWarning: Mean of empty slice”
Any advice on how to circumvent this? I’m getting large regions of just black on the heatmap. Ran identical code yesterday and didn’t see these black regions.
Thanks,
Ben
For reference, here is my code:
bed="/project/juddrice_462/bweekley/nChIP2/peaks/UP_HA_147.05_broad_noCtrl_fdr_0.1_peaks.broadPeak"
bed2="/project/juddrice_462/bweekley/nChIP2/peaks/Cs1Ctrl/UP_HA_147.05_broad_Cs1Ctrl_fdr_0.1_peaks.broadPeak"
Input="/project/juddrice_462/bweekley/nChIP2/bigwigs"
cd $Input
Output="/project/juddrice_462/bweekley/nChIP2/heatmaps"
cd $Output
BL="/scratch2/bweekley/bweekley/genomes/hg19-blacklist.v2.bed"
module load gcc/11.2.0
module load python/3.9.6
computeMatrix reference-point
–referencePoint=center
-S $Input/UP_HA_nomixnodisc1k.sorted_uniq_rmdup.RPKM.bs10.sl30.bw $Input/GSE121840_MOAM-U20S-NS_ALL.bw $Input/UP_Cs1_nomixnodisc1k.sorted_uniq_rmdup.RPKM.bs10.sl30.bw
-R $bed
–samplesLabel U2OS+MMP2_HA U2OS_ATAC U2OS+MMP2_Cs1
-a 4000 -b 4000
-p max
–outFileName “$Output/HAbroadpeaks_U2OS_ATAC_4kb.gz”
–outFileNameMatrix “$Output/HAbroadpeaks_U2OS_ATAC_4kb.txt”
–binSize 50
–skipZeros
–sortUsing=mean
plotHeatmap
-m HAbroadpeaks_U2OS_ATAC_4kb.gz
–colorMap Blues
–colorList white,darkblue
–sortRegions descend
–sortUsingSamples 1
–interpolationMethod nearest
–heatmapHeight 60 --heatmapWidth 10
-min 0 0 0 -max 50 1 50
–yMin 0 0 0 --yMax 50 1 50
–sortUsingSamples 1
-o HAbroadpeaks_U2OS_ATAC_4kb.png
–outFileSortedRegions HAbroadpeaks_U2OS_ATAC_4kb.bed
@bweekley It sounds like this was related to the /project file system being down, which was fixed. Does the code work now?