Post by elias on Feb 7, 2016 18:45:41 GMT
Hi!
Good morning!
I am currently running a GREML-LDMS analysis on 27K samples and 13M SNPs.
This is the command line I submitted:
gcta64 --bfile new_GCTA-GWAS.1000g_20M-imputation.QC --ld-score-region 200 --out new_GCTA-GWAS.1000g_20M-imputation.QCb
and here is the current progression of the analysis:
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.25.2
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Mon Feb 1 10:40:29 2016
Options:
--bfile new_GCTA-GWAS.1000g_20M-imputation.QC
--ld-score-region
--thread-num 2
--out new_GCTA-GWAS.1000g_20M-imputation.QC
Note: the program will be running on 2 threads.
Reading PLINK FAM file from [new_GCTA-GWAS.1000g_20M-imputation.QC.fam].
27065 individuals to be included from [new_GCTA-GWAS.1000g_20M-imputation.QC.fam].
Reading PLINK BIM file from [new_GCTA-GWAS.1000g_20M-imputation.QC.bim].
13502839 SNPs to be included from [new_GCTA-GWAS.1000g_20M-imputation.QC.bim].
Reading PLINK BED file from [new_GCTA-GWAS.1000g_20M-imputation.QC.bed] in SNP-major format ...
Genotype data for 27065 individuals and 13502839 SNPs to be included from [new_GCTA-GWAS.1000g_20M-imputation.QC.bed].
Calculating LD score between SNPs (block size of 10000Kb with an overlap of 5000Kb between blocks); LD rsq threshold = 0) ...
Calculating allele frequencies ...
I was wondering if it would be possible to know the progression of the analysis like PLINK does. I would like to know if the analysis is 10% or 80% complete.
This job has been running for over 5 days and our cluster can only handle up to 2 parallel nodes per job.
This is the memory currently use:
cpu=183:55:40, mem=153750581.57229 GB s, io=85.37757 GB, vmem=236.145G, maxvmem=275.522G
and my current hard resource:
hard resource_list: h_vmem=400G,h_rt=720000
It would be really useful to implement the percentage progression in the next version of GCTA.
Thank you for letting me know if there is anyway I can improve my job request.
Best,
Elias
Good morning!
I am currently running a GREML-LDMS analysis on 27K samples and 13M SNPs.
This is the command line I submitted:
gcta64 --bfile new_GCTA-GWAS.1000g_20M-imputation.QC --ld-score-region 200 --out new_GCTA-GWAS.1000g_20M-imputation.QCb
and here is the current progression of the analysis:
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.25.2
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Mon Feb 1 10:40:29 2016
Options:
--bfile new_GCTA-GWAS.1000g_20M-imputation.QC
--ld-score-region
--thread-num 2
--out new_GCTA-GWAS.1000g_20M-imputation.QC
Note: the program will be running on 2 threads.
Reading PLINK FAM file from [new_GCTA-GWAS.1000g_20M-imputation.QC.fam].
27065 individuals to be included from [new_GCTA-GWAS.1000g_20M-imputation.QC.fam].
Reading PLINK BIM file from [new_GCTA-GWAS.1000g_20M-imputation.QC.bim].
13502839 SNPs to be included from [new_GCTA-GWAS.1000g_20M-imputation.QC.bim].
Reading PLINK BED file from [new_GCTA-GWAS.1000g_20M-imputation.QC.bed] in SNP-major format ...
Genotype data for 27065 individuals and 13502839 SNPs to be included from [new_GCTA-GWAS.1000g_20M-imputation.QC.bed].
Calculating LD score between SNPs (block size of 10000Kb with an overlap of 5000Kb between blocks); LD rsq threshold = 0) ...
Calculating allele frequencies ...
I was wondering if it would be possible to know the progression of the analysis like PLINK does. I would like to know if the analysis is 10% or 80% complete.
This job has been running for over 5 days and our cluster can only handle up to 2 parallel nodes per job.
This is the memory currently use:
cpu=183:55:40, mem=153750581.57229 GB s, io=85.37757 GB, vmem=236.145G, maxvmem=275.522G
and my current hard resource:
hard resource_list: h_vmem=400G,h_rt=720000
It would be really useful to implement the percentage progression in the next version of GCTA.
Thank you for letting me know if there is anyway I can improve my job request.
Best,
Elias