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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
439 stars 98 forks source link

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