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MannLabs / CKG

Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical databases 2) automate knowledge discovery making use of all the information contained in the graph
MIT License
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Graph builder killed without any error thrown #61

Closed victorconan closed 3 years ago

victorconan commented 3 years ago

Hi I got an issue when running

python builder.py --build_type full --download True --user neo4j

The builder was killed without any error thrown:

100% [...................................................] 126835 / 126835Done Parsing database DrugBank
Downloading https://stringdb-static.org/download/protein.aliases.v11.0/9606.protein.aliases.v11.0.txt.gz /home/user/CKG/data/databases/STRING
100% [.............................................] 450734725 / 450734725Killed

And I checked the graph builder log under CKG/logs, it is empty.

Do you know what could cause this issue? Thanks!

victorconan commented 3 years ago

I figured it out. It is out of memory issue. I think the memory should be 32g