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2 hours ago by

Hi,

I am trying to run findPeak in Homer to identify peaks in my ATAC-seq data

The command is as follows

findPeaks <tag directory=""> -style factor -size 200 -minDist 200 -o <output file="">

The job is killed after finding peaks in chromosomes. The output is below.

Fragment Length = 174
Total Tags = 18050226.0
Tags per bp = 0.009025
Max tags per bp set automatically to 1.0
Finding peaks of size 200, no closer than 200
    Finding peaks on chr1 (minCount=0.8), total tags positions = 1352085
    Finding peaks on chr2 (minCount=0.8), total tags positions = 1346939
    Finding peaks on chr3 (minCount=0.8), total tags positions = 1073310
    Finding peaks on chr4 (minCount=0.8), total tags positions = 1098759
    Finding peaks on chr5 (minCount=0.8), total tags positions = 1068535
    Finding peaks on chr6 (minCount=0.8), total tags positions = 1033775
    Finding peaks on chr7 (minCount=0.8), total tags positions = 991290
    Finding peaks on chr8 (minCount=0.8), total tags positions = 917497
    Finding peaks on chr9 (minCount=0.8), total tags positions = 932295
    Finding peaks on chr10 (minCount=0.8), total tags positions = 935931
    Finding peaks on chr11 (minCount=0.8), total tags positions = 1071517
    Finding peaks on chr12 (minCount=0.8), total tags positions = 802788
    Finding peaks on chr13 (minCount=0.8), total tags positions = 791362
    Finding peaks on chr14 (minCount=0.8), total tags positions = 792275
    Finding peaks on chr15 (minCount=0.8), total tags positions = 753944
    Finding peaks on chr16 (minCount=0.8), total tags positions = 709616
    Finding peaks on chr17 (minCount=0.8), total tags positions = 685857
    Finding peaks on chr18 (minCount=0.8), total tags positions = 634591
    Finding peaks on chr19 (minCount=0.8), total tags positions = 487056
    Finding peaks on chrX (minCount=0.8), total tags positions = 559151
    Finding peaks on chrY (minCount=0.8), total tags positions = 2959
    Finding peaks on chrM (minCount=0.8), total tags positions = 8692
            Killed

Any suggestions?



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