Open mandyfrazier opened 5 years ago
Hi @mandyfrazier!
Ah, we need to increase the memory we allow Trinity to use by specifying some parameters in your config.yaml
file.
steps:
./run_eelpond config.yaml trinity --print_params
to print trinity parameters to the terminal. Note that config.yaml
is a placeholder here, and nothing happens to it.config.yaml
file, and modify the max_memory
parameter to suit your needs. Trinity recommends ~1G per million reads. You'll probably need less because we do some digital normalization prior to the trinity step.--threads
and specify the number of cpu you want to use (you might be doing this already).This doc explains in a bit more detail: https://dib-lab.github.io/eelpond/trinity , but also let me know if you have further questions
Thanks @bluegenes for the suggestions, assembly was successful after increasing CPU and GB in the yaml file!
Hi @bluegenes! I tried running eelpond with four samples (~142 million reads total) and it is failing somewhere in Trinity, but I can't actually see the error. I'm thinking that I have a memory issue, but do you have any other suggestions apart from increasing the instance size? Right now the Trinity log file is empty:
cat burbot_assemble_out__experiment1/logs/trinity/trinity.log
This is the error I have access to because I was running it in screen: