Error in system(CMD, intern = TRUE, ignore.stderr = TRUE) : 'perl' not found

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tarek Mohamed

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Apr 26, 2017, 12:00:15 PM4/26/17
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Hi All,

I am trying to use mosaics package to call peaks for my chip-seq experiment. however I got an error message saying "perl not found", how can I resolve this

>library("mosaics")
>constructBins( infile="input_bowtie_sorted.bed" , fileFormat="bed")
>constructBins(infile="input_bowtie_sorted.bed", fileFormat="bed", outfileLoc="./",byChr=FALSE, useChrfile=FALSE,
              chrfile=NULL, excludeChr=NULL, PET=FALSE,capping=0)
------------------------------------------------------------
Info: setting summary
------------------------------------------------------------
Name of aligned read file: input_bowtie_sorted.bed 
Aligned read file format: BED 
Directory of processed bin-level files: ./ 
Construct bin-level files by chromosome? N 
Is file for chromosome info provided? N 
Data type: Single-end tag (SET)
Average fragment length: 200 
Bin size: 200 
------------------------------------------------------------
Error in system(CMD, intern = TRUE, ignore.stderr = TRUE) : 
  'perl' not found


Thanks
Tarek
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