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Copy path[1554763502304] Chromosome 1 Assembly B37.log
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[1554763502304] Chromosome 1 Assembly B37.log
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[2019-04-09 02:45:02,305] : Package Versions
scikit-allel : 1.2.0
matplotlib : 3.0.3
numpy : 1.16.2
pandas : 0.24.2
seaborn : 0.9.0
umap : 0.3.8
[2019-04-09 02:45:02,305] : Parameters Passed
log_dir : ./logs/
plot_dir : ./plots/
coords_dir : ./coords/
genedata : data/ALL.wgs.nhgri_coriell_affy_6.20140825.genotypes_has_ped.vcf
labels : data/affy_samples.20141118.panel
pops : data/20131219.populations.tsv
seed : 42
downsample_n : 10000
prune_size : 500
prune_step : 200
prune_thresh : 0.1
prune_iter : 5
pca_n : 10
pca_scaler : patterson
plot_limit_components : 4
title : Chromosome 1 Assembly B37
[2019-04-09 02:45:15,129] : Loaded Genotype Data from file data/ALL.wgs.nhgri_coriell_affy_6.20140825.genotypes_has_ped.vcf
[2019-04-09 02:45:17,990] : Filtered Genotype Data
[2019-04-09 02:45:22,641] : Applied downsampling to data
[2019-04-09 02:46:01,137] : Pruning iteration 1 retaining 4773 removing 5227 variants
[2019-04-09 02:46:38,372] : Pruning iteration 2 retaining 4743 removing 30 variants
[2019-04-09 02:47:15,760] : Pruning iteration 3 retaining 4742 removing 1 variants
[2019-04-09 02:47:53,206] : Pruning iteration 4 retaining 4742 removing 0 variants
[2019-04-09 02:48:30,745] : Pruning iteration 5 retaining 4742 removing 0 variants
[2019-04-09 02:48:30,775] : Applied pruning with paramaters, size : 500, step : 200, threshold : 0.1, n_iter : 5
[2019-04-09 02:48:35,393] : Applied PCA with 10 components with scaler patterson and seed 42
[2019-04-09 02:48:35,431] : Saved coordinates to ./coords/[1554763502304] Chromosome 1 Assembly B37/[1554763502304] Chromosome 1 Assembly B37 - [PCA] coords.txt
[2019-04-09 02:49:03,434] : Applied UMAP
[2019-04-09 02:49:03,446] : Saved coordinates to ./coords/[1554763502304] Chromosome 1 Assembly B37/[1554763502304] Chromosome 1 Assembly B37 - [UMAP] coords.txt
[2019-04-09 02:49:08,744] : Applied UMAP on PCA reduced space
[2019-04-09 02:49:08,755] : Saved coordinates to ./coords/[1554763502304] Chromosome 1 Assembly B37/[1554763502304] Chromosome 1 Assembly B37 - [UMAP_PCA] coords.txt
[2019-04-09 02:49:08,771] : Constructed dictionary of population codes to population descriptions from data/20131219.populations.tsv
[2019-04-09 02:49:08,771] : Loaded descriptions from data/20131219.populations.tsv
[2019-04-09 02:49:10,108] : Constructed dictionary of samples to population codes from data/affy_samples.20141118.panel
[2019-04-09 02:49:10,109] : Loaded samples mapping from data/affy_samples.20141118.panel
[2019-04-09 02:49:10,153] : Loaded coordinates from ./coords/[1554763502304] Chromosome 1 Assembly B37/[1554763502304] Chromosome 1 Assembly B37 - [PCA] coords.txt
[2019-04-09 02:49:10,153] : Plotting for 4 components
[2019-04-09 02:49:10,363] : Saving plot of PC1 vs PC2
[2019-04-09 02:49:10,976] : Saving plot of PC1 vs PC3
[2019-04-09 02:49:11,523] : Saving plot of PC1 vs PC4
[2019-04-09 02:49:12,076] : Saving plot of PC2 vs PC3
[2019-04-09 02:49:12,641] : Saving plot of PC2 vs PC4
[2019-04-09 02:49:13,257] : Saving plot of PC3 vs PC4
[2019-04-09 02:49:13,817] : Loaded coordinates from ./coords/[1554763502304] Chromosome 1 Assembly B37/[1554763502304] Chromosome 1 Assembly B37 - [UMAP] coords.txt
[2019-04-09 02:49:13,818] : Plotting for 2 components
[2019-04-09 02:49:13,893] : Saving plot of PC1 vs PC2
[2019-04-09 02:49:14,393] : Loaded coordinates from ./coords/[1554763502304] Chromosome 1 Assembly B37/[1554763502304] Chromosome 1 Assembly B37 - [UMAP_PCA] coords.txt
[2019-04-09 02:49:14,394] : Plotting for 2 components
[2019-04-09 02:49:14,464] : Saving plot of PC1 vs PC2
[2019-04-09 02:49:14,981] : Elapsed Time
PCA : 4645 ms
UMAP : 28015 ms
UMAP_PCA : 5309 ms
Total : 252 s