Memory needed to run? - Githubissues

kunalkathuria / SVXplorer

Structural Variant Caller

MIT License

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Memory needed to run? #95

Closed Solyris83 closed 4 years ago

Solyris83 commented 4 years ago

Hi, I have been trying to run SVXplorer a few times already and it keeps getting "Killed" on an ec2 instance with 4 core and 32GB ram. May I know what is the recommended hardware needed to run this?

kunalkathuria commented 4 years ago

Hi,

SVXplorer runs on 1 core. Table 6 in https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007737&type=printable lists peak memory usage for different data sets. What is the coverage of the data set you are using? Can you evaluate peak memory (https://gist.github.com/netj/526585) and report corresponding entry in the "run.log" file, at the time of peak usage?