HOMER Motif Analysis-- homer2 error

Question

[HypoGG]

I am using the HOMER in Cygwin64 terminal, trying to find out motif sites in a subset of gene, http://homer.ucsd.edu/homer/microarray/index.html

I am using the code as follow, $ findMotifs.pl "C:\cygwin64\home\users\bin\BATKO.txt" mouse "C:\cygwin64\home\users\bin\Results" -start -400 -end 100

    Progress: Step1 - Convert input file to refseq IDs
    Percentage of IDs converted into refseq: 96.0% (121 out of 126)

    Progress: Step2 - prepare sequence files

    Progress: Step3 - creating foreground/background file

    Progress: Step4 - removing redundant promoters
            Kept 31006 of 34608

    Progress: Step5 - adjusting background sequences for GC/CpG content...
    Bin     # Targets       # Background    Background Weight
    3       1       927     0.284
    4       8       1675    1.257
    5       13      2799    1.222
    6       22      3760    1.540
    7       45      10494   1.128
    8       19      8046    0.621
    9       7       2558    0.720

    Normalizing lower order oligos using homer2

sh: line 1: \cygwin64\home\kmung\bin/homer2: cannot execute binary file: Exec format error

It looks fine in the beginning and all in sudden it pops out the error message ''cannot execute binary file: Exec format error''. Did anyone also encounter this kind of situation and how should I deal with it?

Sincere thanks!

[Trivas]

Could be a weird syntax difference between \ and /, see \cygwin64\home\kmung\bin/homer2

[Quân]

Hi @HypoGG, I have also encountered the same error. I wonder whether you have found the solution for this matter and will you able to share it? Thanks in advance

[ATpoint]

My first approach would always be to run this in native Linux via WSL2. It is probably some cygwin thing that goes away once it is pure Linux.