Skip to content
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

snpEff build fails with "Out of memory" #14

Closed
verku opened this issue Apr 25, 2022 · 0 comments · Fixed by #21 or #23
Closed

snpEff build fails with "Out of memory" #14

verku opened this issue Apr 25, 2022 · 0 comments · Fixed by #21 or #23
Assignees
Labels
bug Something isn't working enhancement New feature or request

Comments

@verku
Copy link
Collaborator

verku commented Apr 25, 2022

For a user, the rule build_snpEff_db failed due to out of memory.

She'll test the following:

java -jar -Xmx64g /usr/local/share/snpeff-4.3.1t-3/snpEff.jar build -gtf22 -c {params.abs_config} -dataDir {params.abs_data_dir} -treatAllAsProteinCoding -v {params.ref_name} 2> {log}

If it works, update all snpEff rules with the java -jar -Xmx flags and automatic calculation of memory from the number of threads (like QualiMap and Picard)

@verku verku added bug Something isn't working enhancement New feature or request labels Apr 25, 2022
@verku verku self-assigned this Apr 25, 2022
@verku verku linked a pull request Jul 13, 2022 that will close this issue
verku added a commit that referenced this issue Jul 13, 2022
SnpEff using -Xmx for large genomes, closing issue #14
@verku verku closed this as completed Jul 13, 2022
@verku verku linked a pull request Aug 19, 2022 that will close this issue
@verku verku reopened this Aug 19, 2022
@verku verku closed this as completed in #23 Sep 5, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working enhancement New feature or request
Projects
None yet
1 participant