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Steven-N-Hart / vcf-miner

VCF-Miner: A graphical user interface for sorting, filtering and querying annotated VCF Files
MIT License
37 stars 11 forks source link

VCF-miner timeout #15

Closed psddia closed 6 years ago

psddia commented 6 years ago

I'm loading a large CVF file and every time my computer goes to screensaver or I logout, VCF-miner times out. Is there a way to prevent this? Also, how do I save my uploaded VCF files so that I don't have to reload them every time?

psddia commented 6 years ago

I'm also getting an error of "ran out of memory". How do I increase the size?

Steven-N-Hart commented 6 years ago

What is the vcf file size and what are your computer specs?

psddia commented 6 years ago

Huge, 4.7gb in the .gz compressed file which turns into 39gb uncompressed. I have an i7 with 16gb ram. Do I need to run it on the cluster? Does vcfminer use all available cores and ram as defualt?

Steven-N-Hart commented 6 years ago

I've got a message out to one of my colleagues, but it sounds like the file is too big for your machine.

psddia commented 6 years ago

As I've looked at the container messages in kinematic, I think it is a pure memory problem. But, I've downloaded the 3 smallest files from 1000genomes and only the mitochondria and Y file will load. The chromosome 22 file errors. And that file is only ~200MB.

How can I check to see what size RAM is allocated to Miner?

psddia commented 6 years ago

https://i.imgur.com/9CvMzm4.png

then this...

https://i.imgur.com/B8DI8bq.png it happened at 70% https://i.imgur.com/eBW4Aym.png

kitematic says "failed to write...no space left on device" https://i.imgur.com/w2j35n2.png

Steven-N-Hart commented 6 years ago

Ok. This explains it. Your hard drive is too full, so you can't create the database. No database, no app. You need a larger hard drive or freeup more space.