# Snp\_matrix \<- fread("File.raw") Out of Memory

**URL:** <https://discuss.hail.is/t/snp-matrix-fread-file-raw-out-of-memory/4202>\
**Category:** Hail Query & hailctl\
**Created:** [September 6, 2025, 5:00pm UTC](https://discuss.hail.is/t/snp-matrix-fread-file-raw-out-of-memory/4202 "2025-09-06T17:00:25Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![HugHo](https://avatars.discourse-cdn.com/v4/letter/h/b5a626/32.png) [@HugHo](https://discuss.hail.is/u/HugHo)\
**Post date:** [September 6, 2025, 5:00pm UTC](https://discuss.hail.is/t/snp-matrix-fread-file-raw-out-of-memory/4202/1 "2025-09-06T17:00:25Z")

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Hello,  
I would like to perform a GWAS and I already have the .map and raw. files with the phenotype file but the raw file weight 4Go ( output ls -l on puhti server -rw-rw---- 1 huguetho huguetho 4004201413 Aug 4 13:10 All\_samples\_imputed.raw).

I first tried to upload the file under Rstudio but it’s out of memory so then I tried directly on puhti but same and then by a pipeline but I still have error and the GWAS didn’t work. Maybe missing something.  
Does anyone can advice me about GWAS on huge data ? How to perform the model and display Manhattan and QQ plot ?

Best

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**Author:** ![patrick-schultz](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/patrick-schultz/32/265_2.png) [@patrick-schultz](https://discuss.hail.is/u/patrick-schultz)\
**Post date:** [October 29, 2025, 7:54pm UTC](https://discuss.hail.is/t/snp-matrix-fread-file-raw-out-of-memory/4202/2 "2025-10-29T19:54:54Z")

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Hi @HugHo,

Sorry, but this question doesn’t look like it’s about the [Hail](https://hail.is) software. This forum is specifically for help with Hail, not general computational genomics.

Hail is an excellent option for computing GWAS on huge data; see for instance our [tutorial](https://hail.is/docs/0.2/tutorials/01-genome-wide-association-study.html).