stdout_eqtlbma.txt

stdout_eqtlbma.txt

START eqtlbma 2014-10-23 15:43:38
version 1.2 compiled Oct 23 2014 15:01:56
cmd-line: eqtlbma --geno list_genotypes.txt --scoord snp_coords.bed.gz --pheno list_explevels.txt --fcoord gene_coords.bed.gz --anchor TSS --cis 1000 --out out_eqtlbma --step 3 --covar list_covariates.txt --gridL grid_phi2_oma2_general.txt --gridS grid_phi2_oma2_with-configs.txt --bfs all --mvlr
cwd: /home/mike/my_packages/eqtlbma-git/eqtlbma_tutorial_data
load file list_explevels.txt ...
items loaded: 3
load file list_genotypes.txt ...
items loaded: 3
load samples ...
nb of samples (phenotypes): 200
s1 (tissue1): 200 samples
s2 (tissue2): 200 samples
s3 (tissue3): 200 samples
nb of samples (genotypes): 200
s1 (tissue1): 200 samples
s2 (tissue2): 200 samples
s3 (tissue3): 200 samples
total nb of samples: 200
load covariates ...
load file list_covariates.txt ...
items loaded: 3 files for 3 subgroups
s1 (tissue1, 1 file): 1 covariate
s2 (tissue2, 1 file): 1 covariate
s3 (tissue3, 1 file): 1 covariate
load feature coordinates ...
total nb of features with coordinates: 1000
load phenotypes ...
s1 (tissue1, /home/mike/my_packages/eqtlbma-git/eqtlbma_tutorial_data/explevels_tissue1.txt.gz): 1000 features (to keep: 1000)
s2 (tissue2, /home/mike/my_packages/eqtlbma-git/eqtlbma_tutorial_data/explevels_tissue2.txt.gz): 1000 features (to keep: 1000)
s3 (tissue3, /home/mike/my_packages/eqtlbma-git/eqtlbma_tutorial_data/explevels_tissue3.txt.gz): 1000 features (to keep: 1000)
total nb of features to analyze: 1000
load SNP coordinates ...
total nb of SNPs with coordinates: 50186 (loaded in 0.13 sec)
load genotypes ...
s1 (tissue1, /home/mike/my_packages/eqtlbma-git/eqtlbma_tutorial_data/genotypes.txt.gz): 50186 SNPs (to keep: 50186, loaded in 5.56 sec)
duplicate genotypes for other subgroups (same file) ...
s2 (tissue2): 50186 SNPs duplicated in 0.05 sec
s3 (tissue3): 50186 SNPs duplicated in 0.06 sec
total nb of SNPs to analyze: 50186
load grid in grid_phi2_oma2_general.txt ...
grid size: 25
load grid in grid_phi2_oma2_with-configs.txt ...
grid size: 10
look for association between each pair feature-SNP ...
anchor=TSS lenCis=1000 multivariate=true propFitSigma=0.00
==================================================100.00% (1.48 sec)
nb of analyzed feature-SNP pairs: 0 (0 features)
write results of Bayes Factors (one per configuration) ...
file out_eqtlbma_l10abfs_avg-grids.txt.gz
END eqtlbma 2014-10-23 15:43:46
elapsed -> 0d 0h 0m 8s
max.mem -> 278684 kB