I have some chip seq data in BAM format At some point I wanted to do a de novo motif discovery using HOMERs findMotifsGenome.pl script
The problem seems to be that this app cannot open the refrence genome fasta files, even though they were installed by the app itself!
Has anyone encountered this problem?
The linux command used:
$perl /home/chipseq_project/homer/bin/findMotifsGenome.pl /home/chipseq_project/homer/findpeak_output/peaks.txt hg19 /home/chipseq_project/homer/motif_output/ -size given
the stdout text:
Position file = /home/chipseq_project/homer/findpeak_output/peaks.txt
Genome = hg19
Output Directory = /home/chipseq_project/homer/motif_output/
Using actual sizes of regions (-size given)
Fragment size set to given
Found mset for "human", will check against vertebrates motifs
Peak/BED file conversion summary:
BED/Header formatted lines: 0
peakfile formatted lines: 7662
Peak File Statistics:
Total Peaks: 7662
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!
Background fragment size set to 81 (avg size of targets)
Background files for 81 bp fragments found.
Extracting sequences from directory: /home/chipseq_project/homer/.//data/genomes/hg19//
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Not removing redundant sequences
Sequences processed:
0 total
Frequency Bins: 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.6 0.7 0.8
Freq Bin Count
Total sequences set to 50000
Choosing background that matches in CpG/GC Content...
Illegal division by zero at /home/chipseq_project/homer/bin/assignGeneWeights.pl line 63. Assembling sequence file... Normalizing lower order oligos using homer2
Reading input files...
0 total sequences read
Autonormalization: 1-mers (4 total)
A inf% inf% -nan
C inf% inf% -nan
G inf% inf% -nan
T inf% inf% -nan
Autonormalization: 2-mers (16 total)
AA inf% inf% -nan
CA inf% inf% -nan
GA inf% inf% -nan
TA inf% inf% -nan
AC inf% inf% -nan
CC inf% inf% -nan
GC inf% inf% -nan
TC inf% inf% -nan
AG inf% inf% -nan
CG inf% inf% -nan
GG inf% inf% -nan
TG inf% inf% -nan
AT inf% inf% -nan
CT inf% inf% -nan
GT inf% inf% -nan
TT inf% inf% -nan
Autonormalization: 3-mers (64 total)
Normalization weights can be found in file: /home/chipseq_project/homer/motif_output//seq.autonorm.tsv
Converging on autonormalization solution:
...............................................................................
Final normalization: Autonormalization: 1-mers (4 total)
A inf% inf% -nan
C inf% inf% -nan
G inf% inf% -nan
T inf% inf% -nan
Autonormalization: 2-mers (16 total)
AA inf% inf% -nan
CA inf% inf% -nan
GA inf% inf% -nan
TA inf% inf% -nan
AC inf% inf% -nan
CC inf% inf% -nan
GC inf% inf% -nan
TC inf% inf% -nan
AG inf% inf% -nan
CG inf% inf% -nan
GG inf% inf% -nan
TG inf% inf% -nan
AT inf% inf% -nan
CT inf% inf% -nan
GT inf% inf% -nan
TT inf% inf% -nan
Autonormalization: 3-mers (64 total)
Finished preparing sequence/group files
----------------------------------------------------------
Known motif enrichment
Reading input files...
0 total sequences read
264 motifs loaded
Cache length = 11180
Using binomial scoring
Checking enrichment of 264 motif(s)
|0% 50% 100%|
Illegal division by zero at /home/chipseq_project/homer/bin/findKnownMotifs.pl line 142. ---------------------------------------------------------- De novo motif finding (HOMER)
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!!
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!!
-blen automatically set to 2
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!! Use of uninitialized value in numeric gt (>) at /home/chipseq_project/homer/bin/compareMotifs.pl line 1289. !!! Filtered out all motifs!!! Job finished - if results look good, please send beer to ..
Cleaning up tmp files...
