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filter_bam_to_taxa RAM #128

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Jun 23, 2020
Merged

filter_bam_to_taxa RAM #128

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8 changes: 6 additions & 2 deletions pipes/WDL/tasks/tasks_metagenomics.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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} . \
Expand Down Expand Up @@ -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
Expand All @@ -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"
}

}
Expand Down