Question: Empty output when use HOMER annotatePeak.pl
0
gravatar for deb0612
6 weeks ago by
deb06120
deb06120 wrote:

when I use the following command USAGE: perl bin/annotatePeaks.pl 9A26_MarkDuplicates_summits.bed hg38

I got massage below

=====================================================

Peak file = RCC/ATAC-seq/9A26_MarkDuplicates_summits.bed

Genome = hg38

Organism = human

sh: 1: bed2pos.pl: not found

sh: 1: checkPeakFile.pl: not found

sh: 1: cleanUpPeakFile.pl: not found

Reading Positions...

Finding Closest TSS...

sh: 1: annotateRelativePosition.pl: not found

sh: 1: assignGenomeAnnotation: not found

readline() on closed filehandle IN at bin/annotatePeaks.pl line 3230.

rm: cannot remove '0.431673301224695.tmp': No such file or directory

NOTE: If this part takes more than 2 minutes, there is a good chance your machine ran out of memory: consider hitting ctrl+C and rerunning the command with "-noann" To capture annotation stats in a file, use "-annStats <filename>" next time

sh: 1: assignGenomeAnnotation: not found

readline() on closed filehandle IN at bin/annotatePeaks.pl line 3263. Counting Tags in Peaks from each directory... Organism: human Loading Gene Informaiton... Outputing Annotation File...

PeakID (cmd=annotatePeaks.pl RCC/ATAC-seq/9A26_MarkDuplicates_summits.bed hg38)

Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type

Done annotating peaks file

===========================================

There are only headers in the output file.

Why it warned me

sh: 1: bed2pos.pl: not found

sh: 1: checkPeakFile.pl: not found

sh: 1: cleanUpPeakFile.pl: not found

Blockquote

chip-seq software error • 157 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by deb06120

Best guess, the folder with these scripts is not in $PATH.

ADD REPLYlink written 6 weeks ago by ATpoint28k

You need to add a homer bin directory in your executable path (ex.: .bashrc).

Follow the instructions given on the homer installation page.

Look for subsection 4. under Installing the basic HOMER software section on the homer installation page.

Thanks.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Nitin Narwade440
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