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in export_auspice_json parameterize task mem, raise default to 64GB; increase AUGUR_RECURSION_LIMIT from 10k to 15k #429

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Jun 16, 2022
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in export_auspice_json parameterize task mem, raise default to 64GB; increase AUGUR_RECURSION_LIMIT from 10k to 15k #429

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7 changes: 4 additions & 3 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -1688,6 +1688,7 @@ task export_auspice_json {

String out_basename = basename(basename(tree, ".nwk"), "_timetree")

Int? machine_mem_gb
String docker = "nextstrain/base:build-20211012T204409Z"
}

Expand Down Expand Up @@ -1735,7 +1736,7 @@ task export_auspice_json {
echo --auspice-config >> exportargs
echo "~{auspice_config}" >> exportargs

(export AUGUR_RECURSION_LIMIT=10000; cat exportargs | grep . | tr '\n' '\0' | xargs -0 -t augur export v2 \
(export AUGUR_RECURSION_LIMIT=15000; cat exportargs | grep . | tr '\n' '\0' | xargs -0 -t augur export v2 \
~{"--metadata " + sample_metadata} \
~{"--lat-longs " + lat_longs_tsv} \
~{"--colors " + colors_tsv} \
Expand All @@ -1750,10 +1751,10 @@ task export_auspice_json {
>>>
runtime {
docker: docker
memory: "32 GB"
memory: select_first([machine_mem_gb, 64]) + " GB"
cpu : 4
disks: "local-disk 100 HDD"
dx_instance_type: "mem3_ssd1_v2_x4"
dx_instance_type: "mem3_ssd1_v2_x8"
preemptible: 0
maxRetries: 2
}
Expand Down