getDifferentialPeaksReplicates.pl

Question

[jjp55]

Hello,

I am trying to run the Homer command of getDifferentialPeaksReplicates.pl, and it keep failing for me. I have three replicates for my conditions. My command line is

getDifferentialPeaksReplicates.pl -t Treated-1/ Treated-2/ Treated-3/ -i Control-1/ Control-2/ Control-3/ -genome tair10 > Treated_merged_peaks.txt

The program is able to go through the first two steps without a problem, but at Step 3, when calling DESEQ2, I get this error message:

sh: line 1: 39162 Abort trap: 6           R --no-save < "0.971033456808986.edgeR.R" 2> "0.971033456808986.edgeR.out.stderr.txt"
    Warning: Likely a problem with variance stablizing transform
    Often happens without replicates - consider specifying -simpleNorm
    Will report raw counts in output table (no normalization)
rm: 0.971033456808986.edgeR.out.data.txt: No such file or directory
    Using DESeq2 to calculate differential expression/enrichment...
sh: line 1: 39165 Abort trap: 6           R --no-save < "0.971033456808986.edgeR.R" 2> "0.971033456808986.edgeR.out.stderr.txt"
readline() on closed filehandle IN at /Users/mycomputer/opt/anaconda3/bin/getDiffExpression.pl line 926.
!!! Warnining - something likely failed during R execution.
!!! R script that was used:
    ####### basic script for running DESeq (generated by HOMER) ########
    library(DESeq2)
    #Read Data in
    countData <- read.delim("0.971033456808986.edgeR.in.data.txt")
    colData <- read.delim("0.971033456808986.edgeR.groups.data.txt")

    dds <- DESeqDataSetFromMatrix(countData, colData,design=~Treatment,tidy=TRUE)
    libData <- read.delim("0.971033456808986.edgeR.norm.data.txt")

    normFactors <- libData[,2]
    libSizes <- libData[,3]
    colData(dds)$sizeFactor <- normFactors
    dds <- estimateDispersions(dds)
    dds <- nbinomWaldTest(dds)
    res <- results(dds,tidy=TRUE)
    write.table(res,file="0.971033456808986.edgeR.out.data.txt",sep="\t",row.names=FALSE)

!!! R execution details:
    dyld: Library not loaded: @rpath/./libreadline.6.2.dylib
      Referenced from: /Users/mycomputer/opt/anaconda3/lib/R/lib/libR.dylib
      Reason: image not found

I just installed DESEQ2, but am not sure if there is another problem. Any help on this issue is greatly appreciated.