runHomer error

[afcmalone]

Hi,

I am getting no results when i runHomer.

I add pmat to my snapATAC file in R. the peak files (bed) added to the .snap file are in the format chr1 102949 103224 I also tried with bed file in the format b'chr1' 102949 103224 but have the same error

after i runHomer i get 'Illegal division by zero at /home/......../homer/bin//findKnownMotifs.pl line 152.' I think this is because of

Sequences processed: 0 total

given after the peak file is assessed.

Please help :)

here i all my code in R:

motifs = runHomer(

• x.sp[,idy.ls[["3"]],"pmat"],
• mat = "pmat",
• path.to.homer = "/home/......../homer/bin/findMotifsGenome.pl",
• result.dir = "./homer/C3",
• num.cores=5,
• genome = 'hg38',
• motif.length = 10,
• scan.size = 200,
• optimize.count = 2,
• background = 'automatic',
• local.background = FALSE,
• only.known = TRUE,
• only.denovo = FALSE,
• fdr.num = 5,
• cache = 100,
• overwrite = TRUE,
• keep.minimal = FALSE
• );

Position file = ./homer/C3/target_2cec741c5915
Genome = hg38
Output Directory = ./homer/C3
Motif length set at 10,
Fragment size set to 200
Will optimize 2 putative motifs
Using 5 CPUs
Using 100 MB for statistics cache
Will randomize and repeat motif finding 5 times to estimate FDR
Will not run homer for de novo motifs
Found mset for "human", will check against vertebrates motifs
Peak/BED file conversion summary:
    BED/Header formatted lines: 2000
    peakfile formatted lines: 0

Peak File Statistics:
    Total Peaks: 2000
    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 files for 200 bp fragments found.
Custom genome sequence directory: /home/......./homer//data/genomes/hg38//

Extracting sequences from file: /home/......./homer//data/genomes/hg38///genome.fa
Looking for peak sequences in a single file (/home/......../homer//data/genomes/hg38///genome.fa)

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/...../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: ./homer/C3/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
440 motifs loaded
Cache length = 5000
Using binomial scoring
Checking enrichment of 440 motif(s)
|0%                                    50%                                  100%|
=================================================================================

Illegal division by zero at /home/..../homer/bin//findKnownMotifs.pl line 152. Skipping... Job finished - if results look good, please send beer to ..

Cleaning up tmp files...

Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './homer/C3/knownResults.txt': No such file or directory

[ldorozco]

I am getting the same error, but still don't have a solution. I am wondering if this is because I am using hg38 instead of hg19?

[afcmalone]

I tried hg19 and hg38 and get the same error.

On Tue, 28 Jul 2020 at 13:04, ldorozco notifications@github.com wrote:

I am getting the same error, but still don't have a solution. I am wondering if this is because I am using hg38 instead of hg19?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/202#issuecomment-665190752, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM3S4C2TQWNTXGHZKNZJ2ATR54HLVANCNFSM4PFZDMMQ .

[ldorozco]

I figured it out. The 'peaks' GRanges object is messed up, it has "b'" attached to the beginning of each chromosome:

head(x.sp@peak) [1] b'chr1' 191418-192119 | b'chr1':191418-192119 [2] b'chr1' 634093-634293 | b'chr1':634093-634293

If I fIx this GRanges object as follows, Homer can run:

library(stringr) tmp_gr = as.data.frame(x.sp@peak) tmp_seqnames = as.character(tmp_gr[,1]) tmp_seqnames_new = str_replace( str_replace(tmp_seqnames, "b'", ""), "'", "") tmp_gr[,1] = tmp_seqnames_new tmp_names = as.character(tmp_gr[,6]) tmp_names_new = str_replace( str_replace(tmp_names, "b'", ""), "'", "") tmp_gr[,6] = tmp_names_new tmp_gr_new = makeGRangesFromDataFrame(tmp_gr, keep.extra.columns=TRUE) x.sp@peak = tmp_gr_new

[afcmalone]

This works! thanks for the tip!