Hi all,

I've been using homer2 recently, and homer2 can provide new background features. I attempted to use the new function in my data by adding the "-useNewBg" option in findMotifsGenome.pl, but it didn’t work as expected. I also tried running the example data and code provided on the website (http://homer.ucsd.edu/homer/homer2.html) , but I encountered the same error. The error message I received is as follows:

Extracting background sequences from the genome 
terminate called after throwing an instance of 'std::bad_alloc' 
what():  std::bad_alloc

Here is the command I used:

homer2 bg -p tss.positions.200.txt -g hg38.fa -pkmer 2 -N 100000 -NN 10000000 -o ./output

It appears the error maybe related to memory allocation. Despite increasing the memory allocation, I still get the same error. The memory specifications I used are:

#$ -pe sharedmem 1
#$ -l h_vmem=32G

I noticed that on homer2 website they suggest only 8GB when setting -NN 10000000.

I am currently using Homer v5.1, 7-16-2024.

I would be very appreciated to get any suggestions or insights to solve this issue!