Question: Empty output when use HOMER annotatePeak.pl
0
gravatar for deb0612
3 months ago by
deb061210
deb061210 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 • 269 views
ADD COMMENTlink modified 8 days ago • written 3 months ago by deb061210

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

ADD REPLYlink written 3 months ago by ATpoint32k

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 3 months ago • written 3 months ago by Nitin Narwade440
0
gravatar for deb0612
8 days ago by
deb061210
deb061210 wrote:

Thank you! It had been solved.

ADD COMMENTlink written 8 days ago by deb061210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1088 users visited in the last hour