Question: HOMER error -bash: ./ctcf.motif: Permission denied
1
gravatar for gerardo_za_94
7 months ago by
gerardo_za_9410 wrote:

Hello I'm running HOMER on windows through cygwin64. installation was successful, Can run .pl commands.

regardless, it seems that the commands cannot access the motif folder and files within.

don't know how to fix.

Here is the command: $ annotatePeaks.pl DiffBind.noGenes.bed mm10 -size 1000 -hist 10 -m ctcf.motif en1.motif >outfile_anno.txt

outcome:

    Peak file = DiffBind.noGenes.bed
    Genome = mm10
    Organism = mouse
    Peak Region set to 1000
    -----------------------------------------------------
    Histogram mode activated (bin size = 10 bp)
    -----------------------------------------------------
    Motif files:
            ctcf.motif      -m
            en1.motif       -m
    Peak/BED file conversion summary:
            BED/Header formatted lines: 3231
            peakfile formatted lines: 0
            Duplicated Peak IDs: 3230

    Peak File Statistics:
            Total Peaks: 3231
            Redundant Peak IDs: 0
            Peaks lacking information: 0 (need at least 5 columns per peak)
            Peaks with misformatted coordinates: 0 (should be integer)
            Peaks with misformatted strand: 0 (should be either +/- or 0/1)

    Peak file looks good!

    Resizing peaks...
    Extracting Sequence...
    Custom genome sequence directory: /home/gerar/.//data/genomes/mm10/

    Extracting sequences from directory: /home/gerar/.//data/genomes/mm10/
    Extracting 203 sequences from chr1
    Extracting 254 sequences from chr2
    Extracting 281 sequences from chr3
    Extracting 217 sequences from chr4
    Extracting 178 sequences from chr5
    Extracting 235 sequences from chr6
    Extracting 184 sequences from chr7
    Extracting 212 sequences from chr8
    Extracting 140 sequences from chr9
    Extracting 162 sequences from chr10
    Extracting 113 sequences from chr11
    Extracting 151 sequences from chr12
    Extracting 163 sequences from chr13
    Extracting 110 sequences from chr14
    Extracting 143 sequences from chr15
    Extracting 109 sequences from chr16
    Extracting 138 sequences from chr17
    Extracting 82 sequences from chr18
    Extracting 94 sequences from chr19
    Extracting 47 sequences from chrX
    Extracting 14 sequences from chrY
    Extracting 1 sequences from chrUn_GL456378
    Reading Positions...
    Calculating CpG/GC Content of Peaks

    Sequences processed:
            Auto detected maximum sequence length of 1001 bp
            3231 total

    -----------------------
    Looking for Motifs...
    readline() on closed filehandle IN at /home/gerar/bin/annotatePeaks.pl line 1277.

    Reading input files...
    3231 total sequences read
    !!! Couldn't open motif file: ctcf.motif !!!
    Finding instances of 0 motif(s)
    |0%                                    50%                                  100%|

    readline() on closed filehandle IN at /home/gerar/bin/annotatePeaks.pl line 1277.

    Reading input files...
    3231 total sequences read
   !!! Couldn't open motif file: en1.motif !!!
    Finding instances of 0 motif(s)
    |0%                                    50%                                  100%|

    Compiling per bp Histograms...
    Finding Tags in Peaks from each directory...

    Sequences processed:
            3231 total
ADD COMMENTlink modified 7 months ago • written 7 months ago by gerardo_za_9410
2

Where is the error mentioned in title in your post ? Can you check if those files have read permissions ? Also try giving full path.

ADD REPLYlink written 7 months ago by geek_y11k

The path is set to homer\gerar\bin If I set it to gerar --> commands will not be located.

Also, the whole folder and files within, have full permissions.

ADD REPLYlink written 7 months ago by gerardo_za_9410

The error in the title arises from me directly trying to access the motif files within the motif folder

############################################

gerar@nena ~
$ ls

bin                   DoughnutDocumentation.pdf   README.txt
blat                  ghostscript-9.52            SRR8159023.bed
config.txt            motifs                      trialannotatepeaks.txt
configureHomer.pl     Mus_musculus.GRCm38.99.gtf  update
COPYING               outdirmotif_3               update.txt
cpp                   outfile_anno.txt            weblogo
data                  outfile_trial2.txt
DiffBind.noGenes.bed  outfile3.txt

gerar@nena ~
$ cd motifs

gerar@nena ~/motifs
$ ctcf.motf
-bash: ctcf.motf: command not found

 gerar@nena ~/motifs
 $
ADD REPLYlink modified 7 months ago by genomax92k • written 7 months ago by gerardo_za_9410

Sorry, copied the wrong thing

Here is the actual:

########################

gerar@nena ~/motifs
$ ctcf.motif
-bash: ./ctcf.motif: Permission denied

gerar@nena ~/motifs
$
ADD REPLYlink modified 7 months ago by genomax92k • written 7 months ago by gerardo_za_9410

Have no idea what to do, or how to fix. Still getting the same response:

    Extracting 14 sequences from chrY
    Extracting 1 sequences from chrUn_GL456378
    Reading Positions...
    Calculating CpG/GC Content of Peaks

    Sequences processed:
            Auto detected maximum sequence length of 501 bp
            3231 total

    -----------------------
    Looking for Motifs...
    readline() on closed filehandle IN at /home/gerar/bin/annotatePeaks.pl line 1277.

    Reading input files...
    3231 total sequences read
   !!! Couldn't open motif file: ctcf.motif !!!
    Finding instances of 0 motif(s)
    |0%                                    50%                                  100%|

    Compiling per bp Histograms...
    Finding Tags in Peaks from each directory...

    Sequences processed:
            3231 total
ADD REPLYlink written 7 months ago by gerardo_za_9410

Directly input the file name of your motif file cannot tell you if you have access, the shell thinks you are executing a command called "ctcf.motif"

You should use

ls -l

Could you show the output of the above command?

ADD REPLYlink written 7 months ago by yztxwd380
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