

################################################################ miami PROCESS






################################ RUNNING DATE AND STARTING TIME




2024-02-20 14:58:39






################################ RUNNING






################################ RUNNING END




END TIME: 2024-02-20 14:58:46




TOTAL TIME LAPSE: 6S




ALL DATA SAVED IN all_objects.RData




################################ RECAPITULATION OF WARNING MESSAGES




NO WARNING MESSAGE TO REPORT




################################ INITIAL SETTINGS OF PARAMETERS



erase.objects        TRUE 
erase.graphs         TRUE 
script               miami 
run.way              SCRIPT 
command              /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/gmillot/Documents/Git_projects/fisher_for_vcf/bin/miami.R,--args,fisher.tsv,hg19_grch37p5_chr_size_cumul.txt,chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM,FALSE,NEG_LOG10_P_VALUE_CARRIER_MODEL,AF,NULL,NULL,NULL,NULL,FALSE,FALSE,NULL,NULL,FALSE,TRUE,cute_little_R_functions.R,miami_report.txt 
whole                chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM 
fisher               fisher.tsv 
chr.path             hg19_grch37p5_chr_size_cumul.txt 
x.lim                chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM 
vgrid                FALSE 
top.y.column         NEG_LOG10_P_VALUE_CARRIER_MODEL 
bottom.y.column      AF 
color.column         NULL 
dot.border.color     NULL 
y.lim1               NULL 
y.lim2               NULL 
reverse1             FALSE 
reverse2             FALSE 
y.threshold1         NULL 
y.threshold2         NULL 
y.log1               FALSE 
y.log2               TRUE 
cute                 cute_little_R_functions.R 
log                  miami_report.txt




################################ R SYSTEM AND PACKAGES


R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] ggplot2_3.3.3   lubridate_1.8.0 qqman_0.1.8     scales_1.1.1   

loaded via a namespace (and not attached):
 [1] assertthat_0.2.1 calibrate_1.7.7  cli_3.2.0        colorspace_2.0-3
 [5] compiler_4.1.2   crayon_1.5.0     DBI_1.1.2        digest_0.6.29   
 [9] dplyr_1.0.8      ellipsis_0.3.2   fansi_1.0.2      farver_2.1.0    
[13] generics_0.1.2   glue_1.6.2       gridExtra_2.3    gtable_0.3.0    
[17] labeling_0.4.2   lifecycle_1.0.1  magrittr_2.0.2   MASS_7.3-55     
[21] munsell_0.5.0    pillar_1.7.0     pkgconfig_2.0.3  purrr_0.3.4     
[25] R6_2.5.1         rlang_1.0.2      tibble_3.1.6     tidyselect_1.1.2
[29] utf8_1.2.2       vctrs_0.3.8      withr_2.5.0     



