-
Notifications
You must be signed in to change notification settings - Fork 7
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
command "paladin prepare -r2" throwing error related to memory ? #40
Comments
Hello,
Although the Dave |
Hi @davidfbibby - to double check, I just clustered the latest revision of the clustered RVDB (around 3.1 GB of amino acids uncompressed) while profiling the memory usage. The maximum resident size during indexing for this reference is 56GB, but as can be seen above, it actually allocates a larger amount to work in (128GB) so you'll need at least that much (system memory and/or job constraint wise) to complete the indexing process. Does your system have that much memory? |
Hi, Thanks for the quick response, Dave |
Another question - on |
|
Apologies, that's a nucleotide version of the reference at that link! I totally missed that when I downloaded it yesterday. I'll take a look around for a clustered version of the protein database - if not, you may have to cluster it yourself to fit into memory. Sorry again |
Ooof. I don't fancy clustering them. I'll see if I can get more memory to allocate... Dave |
Hi,
Is there any way/hack to run this particular part without encountering this error given below, if you have less memory, in my case 256GB only. Or can I use the pre-prepared or pre-indexed database?
Error: "Constructing BWT for the packed sequence... [is_bwt] Failed to allocate 482146077304 bytes at is.c line 212: Cannot allocate memory"
Kindly suggest.
The text was updated successfully, but these errors were encountered: