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Post by fabian on Feb 4, 2020 8:56:55 GMT
Hi
I have a large dataset (130097 animals x 48292 SNPs)and I'm trying to run a GWAS on it. I'm using GCTA 1.93.0 beta
1: I've tryed to run --fastGWA-mlm after making the sparse GRM but this results in a segmentation fault 2: I've precomputed the GRMs by chrom and have tried to run --mlma-subtract-grm, however running this consumes almost 0.45Tb of memory and finally fails (memory issue I believe)
I would very much appreciate any tips suggestions on how I can use GCTA to analyse this large chunk of data. It really sounds like a task for --fastGWA ..
Thanks, Fabian
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nick
New Member
Posts: 2
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Post by nick on Feb 23, 2020 16:52:39 GMT
I am getting a segmentation fault with the UK Biobank data in bgen format, the autosomes and XY (PAR) work, but the X chromosome causes a seg fault. At first it wasn't working because the Metadata table is missing from the X chrom .bgi file as distributed, so I reindexed the X chromosome with bgenix and now it seg faults.
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dvh13
New Member
Posts: 5
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Post by dvh13 on Apr 9, 2020 15:42:21 GMT
at which stage are you getting seg fault. i am getting this too. will post separately
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