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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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High RAM usage in "seeking" mode. #121

Open titoghose opened 3 years ago

titoghose commented 3 years ago

Hello,

I've been running ExpansionHunter in "seeking" mode for a few hundred variants and I see that the RAM usage keeps increasing and goes up to around 14-16 GB. I was wondering is this can be reduced or controlled in some manner.

egor-dolzhenko commented 3 years ago

I am sorry to hear about the high memory usage. Seeking mode should not be using this much RAM.

Are you using the default repeat catalog? And are you compiling the program yourself or using a precompiled binary?

titoghose commented 3 years ago

Hello, thanks for the response. I am using a custom repeat catalog, testing about 1000 STR. I'm using version 4.0.1, precompiled.

egor-dolzhenko commented 3 years ago

I see. Would it be permissible to share the catalog? If yes, please feel free to send it by email. I can run some benchmarks to see what causes the issue.