Closed CriticalSci closed 4 years ago
Hello!
I don't have a definite answer yet as I've neither tested on CentOS nor have I used 1kb resolution arrays with that function. What happens when you try the overcommit workaround described in the stackoverflow answers? Does it work fine for 5kb or 10kb resolution? I'm also curious to know if cooltools works on the same file.
Hi, the highest resolution I've tested for training so far is 5K. But if you are just trying to calculate the total intra-chromosomal reads, I suggest using lower-resolution matrices. In your case, the command will be peakachu depth -p contactmatrix.mcool::/resolutions/10000
or even peakachu depth -p contactmatrix.mcool::/resolutions/100000
.
Thanks guys, I was able to run the tool on 16K resolution peakachu depth -p H3K27Ac.mcool::/resolutions/16000
:)
I only got about 12.5M intra-reads so I guess I will use the 30M models!
Hi there,
Trying to test out Peakachu on a HPC Cluster with following specs: Processors: 32-cores of Intel(R) Xeon(R) Gold 6142 CPU @ 2.60GHz RAM: 384GB RAM OS: CentOS 7.6
However on running
peakachu depth -p contactmatrix.mcool::/resolutions/1000
with ample memory (NCPUs Requested: 32, NCPUs Used: 32, Memory Requested: 264gb, Memory Used: 212190396kb) I am getting a MemoryError (see below). Seems it may be an issue with overcommit handling?Has anyone ever encountered this problem?