!!! HOMER not configured properly!!!! !!! Could not open /gpfs/data01/cbenner/software/homer/.//config.txt !!!
•
written
by
elshaimaa.ali •
2 answers
Despite having tried the installation guide (v4.10, 5-16-2018), I had the same error when executing,
./findMotifsGenome.pl
Could not open configuration file (/gpfs/data01/cbenner/software/homer/.//config.txt)
I checked perl ../configureHomer.pl and the current base directory for HOMER was ok but still failed.
So, I solved the problem changing two lines in findMotifsGenome.pl and in HomerConfig.pm
use lib "/gpfs/data01/cbenner/software/homer/.//bin";
my $homeDir = "/gpfs/data01/cbenner/software/homer/./";
Hope this helps.
EDIT: It seemed that ./findMotifsGenome.pl worked but due to other dependencies I couldn't run Homer.
EDIT2: a conda environment installing homer is what worked for me.
Regards,
Alicia
Hi Ram,
Thanks for your reply! I'm actually very new to the field of bioinfo and have trouble understanding NGS analysis. I'm trying to run homer for post processing on my directories, to remove out of Bound tags. Here is what the error looks like: https://ibb.co/NyMHdB1 Do you think this is because I didn't set up a conda emvironment?
Thanks in advance!
When you're seeing command line errors, it's best to copy-paste the text and use code formatting. I have not used homer, but it looks like you're missing a resource file, and the tool to create that resource file cannot be executed.
What is the output to
stat /Users/<redacted>/Desktop/Lab/Homer/bin/homerTools
Log in to answer this question.
-
homer installation
written by leslielebon •
-
Loop and TAD calling from HiC reads using HOMER
written by arsala521 •
-
homer not configured properly
written by amahdi779 •
-
Why piping a conda command into bash doesn't work ?
written by Pierre Lindenbaum
-
HOMER on AWS
written by Bogdan
-
HOMER hg19 not found in config.txt
written by jeni •
-
homer makebigwig error
written by yueli7
-
Homer findmotifs.pl keeps failing because it can't find the promoter set which is installed
written by sandKings •
-
Falcon Assembly error - [ERROR]Task Node(1-preads_ovl) failed with exit-code=256
written by David_emir
-
How to avoid problem using -size, -hist and -ghist for annotatePeaks.pl in HOMER?
written by marko.baros •
Hello, would you answer this question if you were not you? Please, explain a little more what you are trying to do. Also, show the full commands that you are using. Failure to do this will likely mean that nobody will attempt to answer your question.
Hello, elshaimaa.ali,
How can you figure out this problem?
Thanks in advance!
Yuw
You should open the findMotifsGenome.pl script and change the path to homer in your system. Hope it helps!
This has already been suggested. Please explain what your answer contributes that previous answers already have not already contributed. Until then, I'm moving your "answer" to a comment.