GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
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)
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)