diff --git a/pipes/WDL/tasks/tasks_metagenomics.wdl b/pipes/WDL/tasks/tasks_metagenomics.wdl index ecb67c5e5..8f10cf18e 100644 --- a/pipes/WDL/tasks/tasks_metagenomics.wdl +++ b/pipes/WDL/tasks/tasks_metagenomics.wdl @@ -657,6 +657,9 @@ task filter_bam_to_taxa { export TMPDIR=$(pwd) fi + # find 90% memory + mem_in_mb=$(/opt/viral-ngs/source/docker/calc_mem.py mb 90) + # decompress taxonomy DB to CWD read_utils.py extract_tarball \ ${ncbi_taxonomy_db_tgz} . \ @@ -690,6 +693,7 @@ task filter_bam_to_taxa { ${true='--without-children' false='' withoutChildren} \ ${'--minimum_hit_groups=' + minimum_hit_groups} \ --out_count COUNT \ + --JVMmemory "$mem_in_mb"m \ --loglevel=DEBUG samtools view -c "${out_basename}.bam" | tee classified_taxonomic_filter_read_count_post @@ -706,10 +710,10 @@ task filter_bam_to_taxa { runtime { docker: "${docker}" - memory: "7 GB" + memory: "13 GB" disks: "local-disk 375 LOCAL" cpu: 2 - dx_instance_type: "mem1_ssd2_v2_x4" + dx_instance_type: "mem3_ssd1_v2_x2" } }