diff --git a/README.md b/README.md
index 17e3fc7cf1428d7bf7ee179b71bd6d93342ba019..0c7694ff7c10050184960bebe3d95bc0b840f567 100644
--- a/README.md
+++ b/README.md
@@ -120,7 +120,7 @@ See chmod in protocol 44.
 Like above but then run the following command from here \\wsl$\Ubuntu-20.04\home\gael:
 
 ```bash
-nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config
+nextflow run -c fisher_for_vcf.config fisher_for_vcf.nf
 ```
 
 with -c to specify the name of the config file used.
@@ -164,7 +164,7 @@ Then run:
 HOME="${ZEUSHOME}/fisher_for_vcf/" ; trap '' SIGINT ; nextflow run --modules ${MODULES} -hub pasteur gmillot/fisher_for_vcf -r v1.0 -c $HOME/fisher_for_vcf.config ; HOME="/pasteur/appa/homes/gmillot/"  ; trap SIGINT
 
 # local fisher_for_vcf.nf file ($HOME changed to allow the creation of .nextflow into /$ZEUSHOME/fisher_for_vcf/. See NFX_HOME in the nextflow soft script)
-HOME="${ZEUSHOME}/fisher_for_vcf/" ; trap '' SIGINT ; nextflow run --modules ${MODULES} fisher_for_vcf.nf -c fisher_for_vcf.config ; HOME="/pasteur/appa/homes/gmillot/" ; trap SIGINT
+HOME="${ZEUSHOME}/fisher_for_vcf/" ; trap '' SIGINT ; nextflow run --modules ${MODULES} -c fisher_for_vcf.config fisher_for_vcf.nf ; HOME="/pasteur/appa/homes/gmillot/" ; trap SIGINT
 ```
 
 If an error message appears, like:
@@ -185,17 +185,19 @@ Copy-paste this into a linux console
 PWD=$(pwd)
 # see the fisher_for_vcf.config file for info about the parameters
 echo -e '
-fisher="dataset/res_fisher.tsv.gz"
-chr="dataset/hg19_grch37p5_chr_size_cumul.txt"
+fisher="${PWD}/dataset/res_fisher.tsv.gz"
+chr="${PWD}/dataset/hg19_grch37p5_chr_size_cumul.txt"
 x_lim="chr1"
 bottom_y_column="AF"
 color_column="NULL"
 y_lim1="NULL"
 y_lim2="NULL"
+y_log1="FALSE"
+y_log2="TRUE"
 cute="https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R"
 
-Rscript bin/miami.R ${fisher} ${chr} "${x_lim_val}" "${bottom_y_column}" "${color_column}" "${y_lim1}" "${y_lim2}" "${cute}" "miami_report.txt"
-' | sudo docker run --workdir /tempo/ -i --mount "type=bind,src=${PWD},dst=/tempo/" --entrypoint bash gmillot/r_v4.1.2_extended_v2.1:gitlab_v8.8
+Rscript ${PWD}/bin/miami.R ${fisher} ${chr} "${x_lim}" "${bottom_y_column}" "${color_column}" "${y_lim1}" "${y_lim2}" "${y_log1}" "${y_log2}" "${cute}" "miami_report.txt"
+' | sudo docker run --workdir /tmp/ -i --mount "type=bind,src=${PWD},dst=/tmp/" --entrypoint bash gmillot/r_v4.1.2_extended_v2.1:gitlab_v8.8
 ```
 
 The outputs files are in $PWD, i.e., where the code has been executed.
@@ -284,6 +286,11 @@ Gitlab developers
 ## WHAT'S NEW IN
 
 
+### v2.3
+
+miamiplot: log10 scale and alignment of graphics
+
+
 ### v2.2
 
 bug fixed in miamiplot
diff --git a/bin/miami.R b/bin/miami.R
index 0bcb1f1853486e713c5c50c1f56685ba06760681..0bcfccd13fc3f0e73749979e5c3d8a9272867c6d 100644
--- a/bin/miami.R
+++ b/bin/miami.R
@@ -82,6 +82,8 @@ if(interactive() == FALSE){ # if(grepl(x = commandArgs(trailingOnly = FALSE), pa
         "color.column",
         "y.lim1", 
         "y.lim2", 
+        "y.log1", 
+        "y.log2", 
         "cute", 
         "log"
     ) # objects names exactly in the same order as in the bash code and recovered in args. Here only one, because only the path of the config file to indicate after the miami.R script execution
@@ -108,17 +110,17 @@ rm(tempo.cat)
 
 # fisher <- "C:/Users/gael/Documents/Git_projects/fisher_for_vcf/dataset/fisher.tsv"
 # chr.path <- "C:/Users/gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt"
-# x.lim <- "chr1:0-50000, chr3:0-150000" # "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"
-# bottom.y.column <- "NULL"
+# 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" # "chr1:0-50000, chr3:0-150000"   
+# bottom.y.column <- "AF"
 # color.column <- "NULL"
-# y.lim1 <- 5
-# y.lim2 <- 3
+# y.lim1 <- "NULL"
+# y.lim2 <- "NULL"
+# y.log1 <- "FALSE"
+# y.log2 <- "FALSE"
 # cute <- "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" 
 # log <- "miami_report.txt"
 
 
-
-
 ################################ end Test
 
 ################################ Recording of the initial parameters
@@ -138,6 +140,8 @@ param.list <- c(
     "color.column",
     "y.lim1", 
     "y.lim2",
+    "y.log1", 
+    "y.log2", 
     "cute", 
     "log"
 )
@@ -219,6 +223,8 @@ if( ! is.null(tempo)){
 req.package.list <- c(
     "lubridate", 
     "ggplot2", 
+    "scales", 
+    "grid", 
     "qqman"
 )
 for(i in 1:length(req.package.list)){suppressMessages(library(req.package.list[i], character.only = TRUE))}
@@ -271,6 +277,7 @@ if(all(y.lim2 != "NULL")){
 }else{
     y.lim2 <- NULL
 }
+tempo <- fun_check(data = y.log1, class = "vector", typeof = "character", length = 1) ; eval(ee)
 tempo <- fun_check(data = log, class = "vector", typeof = "character", length = 1) ; eval(ee)
 if(any(arg.check) == TRUE){ # normally no NA
     stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
@@ -283,6 +290,8 @@ if(any(arg.check) == TRUE){ # normally no NA
 tempo.arg <-c(
     "fisher",
     "chr.path", 
+    "y.log1", 
+    "y.log2", 
     "log"
 )
 tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
@@ -291,6 +300,26 @@ if(any(tempo.log) == TRUE){# normally no NA with is.null()
     stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
 }
 # end management of NULL arguments
+# management of ""
+tempo.arg <-c(
+    "fisher", 
+    "chr.path", 
+    "x.lim", 
+    "bottom.y.column",
+    "color.column",
+    "y.lim1", 
+    "y.lim2",
+    "y.log1", 
+    "y.log2", 
+    "cute", 
+    "log"
+)
+tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = function(x){any(x == "")})
+if(any(tempo.log) == TRUE){# normally no NA with is.null()
+    tempo.cat <- paste0("ERROR IN miami.R:\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE \"\"")
+    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+}
+# end management of ""
 # code that protects set.seed() in the global environment
 # end code that protects set.seed() in the global environment
 # warning initiation
@@ -300,6 +329,22 @@ warn <- NULL
 # warn.count <- 0 # not required
 # end warning initiation
 # other checkings
+if(y.log1 == "TRUE"){
+    y.log1 <- TRUE
+}else if(y.log1 == "FALSE"){
+    y.log1 <- FALSE
+}else{
+    tempo.cat <- paste0("ERROR IN miami.R\ny.log1 PARAMETER CAN ONLY BE \"TRUE\" OR \"FALSE\": ", y.log1)
+    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+}
+if(y.log2 == "TRUE"){
+    y.log2 <- TRUE
+}else if(y.log2 == "FALSE"){
+    y.log2 <- FALSE
+}else{
+    tempo.cat <- paste0("ERROR IN miami.R\ny.log2 PARAMETER CAN ONLY BE \"TRUE\" OR \"FALSE\": ", y.log2)
+    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+}
 # end other checkings
 # reserved word checking
 # end reserved word checking
@@ -317,7 +362,7 @@ warn <- NULL
 ################ Ignition
 
 
-fun_report(data = paste0("\n\n################################################################ miami PROCESS\n\n"), output = log, path = "./", overwrite = FALSE)
+fun_report(data = paste0("\n\n################################################################ miami PROCESS\n\n"), output = log, path = "./", overwrite = TRUE)
 ini.date <- Sys.time()
 ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
 fun_report(data = paste0("\n\n################################ RUNNING DATE AND STARTING TIME\n\n"), output = log, path = "./", overwrite = FALSE)
@@ -511,21 +556,47 @@ if(empty.obs == TRUE){
         assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), scale_colour_gradient2())
     }
     assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(
-        paste0("x.lim: ", ifelse(x.lim == whole, "whole genome", x.lim))
+        paste0("x.lim: ", ifelse(x.lim == whole, "whole genome", x.lim), ifelse(y.log1, ", top y-axis: log10", ""), ifelse(y.log2, ", bottom y-axis: log10", ""))
     ))
     assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), scale_x_continuous(
+        name = "CHR", 
         expand = c(0, 0), # remove space after after axis limits
         oob = scales::rescale_none,
         label = chr$CHR_NAME, 
         breaks= chr$CHR_NAME_POS, 
         limits = c(xmin_plot - marging, max(chr$LENGTH_CUMUL) + marging)
     ))
-    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), scale_y_continuous(
-        expand = c(0, 0), # remove space after after axis limits
-        limits = y.lim1, # NA indicate that limits must correspond to data limits but ylim() already used
-        oob = scales::rescale_none, 
-        trans = "identity" # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
-    ))
+    if(y.log1){
+        if(any(obs$NEG_LOG10_P_VALUE <= 0)){
+            tempo.cat <- paste0("ERROR IN miami.R:\nTHE y_log1 PARAMETER CANNOT BE SET TO \"TRUE\" IF 0 OR NEG VALUES IN THE NEG_LOG10_P_VALUE FIELD OF THE TSV OR VCF")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), scale_y_continuous(
+                expand = c(0, 0), # remove space after after axis limits
+                limits = y.lim1, # NA indicate that limits must correspond to data limits but ylim() already used
+                oob = scales::rescale_none, 
+                trans = "log10",  # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
+                breaks = scales::trans_breaks("log10", function(x){10^x}), 
+                labels = scales::trans_format("log10", scales::math_format(10^.x))
+            ))
+            # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), annotation_logticks(outside = TRUE))
+        }
+    }else{
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), scale_y_continuous(
+            expand = c(0, 0), # remove space after after axis limits
+            limits = y.lim1, # NA indicate that limits must correspond to data limits but ylim() already used
+            oob = scales::rescale_none, 
+            trans = "identity" # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
+        ))
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), annotate(
+            geom = "segment", 
+            x = c(xmin_plot, chr$LENGTH_CUMUL), 
+            xend = c(xmin_plot, chr$LENGTH_CUMUL), 
+            y = 0, 
+            yend = -0.05, 
+            size = 1.5
+        ))
+    }
     assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), theme_bw())
     assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), theme(
         plot.title = ggplot2::element_text(size = 8), 
@@ -535,15 +606,7 @@ if(empty.obs == TRUE){
         panel.grid.minor.x = element_blank(),
         axis.ticks.x = element_blank()
     ))
-    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), annotate(
-        geom = "segment", 
-        x = c(xmin_plot, chr$LENGTH_CUMUL), 
-        xend = c(xmin_plot, chr$LENGTH_CUMUL), 
-        y = 0, 
-        yend = -0.05, 
-        size = 1
-    ))
-    
+
     fin.plot1 <- suppressMessages(suppressWarnings(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))))
     
     if(is.null(bottom.y.column)){
@@ -566,12 +629,29 @@ if(empty.obs == TRUE){
             breaks= chr$CHR_NAME_POS, 
             limits = c(xmin_plot - marging, max(chr$LENGTH_CUMUL) + marging)
         ))
-        assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), scale_y_continuous(
-            expand = c(0, 0), # remove space after after axis limits
-            limits = y.lim2, # NA indicate that limits must correspond to data limits but ylim() already used
-            oob = scales::rescale_none, 
-            trans = "reverse" # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
-        ))
+        if(y.log2){
+            if(any(obs[ , bottom.y.column] <= 0)){
+                tempo.cat <- paste0("ERROR IN miami.R:\nTHE y_log2 PARAMETER CANNOT BE SET TO \"TRUE\" IF 0 OR NEG VALUES IN THE ", bottom.y.column, " FIELD OF THE TSV OR VCF")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), scale_y_continuous(
+                    expand = c(0, 0), # remove space after after axis limits
+                    limits = y.lim2, # NA indicate that limits must correspond to data limits but ylim() already used
+                    oob = scales::rescale_none, 
+                    trans = "log10",  # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
+                    breaks = scales::trans_breaks("log10", function(x){10^x}), 
+                    labels = scales::trans_format("log10", scales::math_format(10^.x))
+                ))
+                # assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), annotation_logticks(outside = TRUE)) # 
+            }
+        }else{
+            assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), scale_y_continuous(
+                expand = c(0, 0), # remove space after after axis limits
+                limits = y.lim2, # NA indicate that limits must correspond to data limits but ylim() already used
+                oob = scales::rescale_none, 
+                trans = "reverse" # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
+            ))
+        }
         assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), theme_bw())
         assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), theme(
             legend.position=if(is.null(color.column)){"none"},
@@ -582,9 +662,12 @@ if(empty.obs == TRUE){
             axis.text.x=element_blank(),
             axis.ticks.x=element_blank()
         ))
+
         fin.plot2 <- suppressMessages(suppressWarnings(eval(parse(text = paste(paste0(tempo.gg.name2, 1:tempo.gg.count2), collapse = " + ")))))
-        
-        suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot1, fin.plot2, ncol=1, nrow = 2)))
+        gl <- lapply(list(fin.plot1, fin.plot2), ggplotGrob)  
+        wd <- do.call(unit.pmax, lapply(gl, "[[", 'widths'))
+        gl <- lapply(gl, function(x){x[['widths']] = wd ; x})
+        suppressMessages(suppressWarnings(gridExtra::grid.arrange(gl[[1]], gl[[2]], ncol=1, nrow = 2)))
     }
 }else{
     fun_gg_empty_graph(text = paste0("NO PLOT DRAWN\nTHE x_lim PARAMETER\nMIGHT BE OUTSIDE\nOF THE RANGE OF THE VCF FILE\nOR THE RANGE OF THE region PARAMETER\nOR NULL"))
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/miami.png b/example_of_results/PL_family_WGS_fisher_1667491523/miami.png
index 496f0296dc9a22592d99636ca57ba979af716e96..9cdbb279ad66cd49092b456c643ff3e167f560c9 100644
Binary files a/example_of_results/PL_family_WGS_fisher_1667491523/miami.png and b/example_of_results/PL_family_WGS_fisher_1667491523/miami.png differ
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/Run_info.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/Run_info.txt
index 6c232b9a586c6266818285f89ba2e0a8ba946655..e1d73f21404f4340945fe9deead4bad7067ca0a9 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/Run_info.txt
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/Run_info.txt
@@ -1,9 +1,9 @@
 Project (empty means no .git folder where the main.nf file is present):  origin git@gitlab.pasteur.fr:gmillot/fisher_for_vcf.git (fetch)
-Git info (empty means no .git folder where the main.nf file is present):  v2.1-dirty
-Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config
+Git info (empty means no .git folder where the main.nf file is present):  v2.2-dirty
+Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume
 execution mode: local
 Manifest's pipeline version: null
-result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1667491523
+result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1667575249
 nextflow version: 21.04.2
 
 
@@ -16,5 +16,5 @@ workDir (directory where tasks temporary files are created): /mnt/c/Users/Gael/D
 
 USER VARIABLES:
 
-out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1667491523
+out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1667575249
 sample_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot b/example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot
index f93eac5e44cee38634adc990094dbb98aeae078d..0eebf451adf2fc7b45c8b874de2e456af75f9eba 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot
@@ -3,17 +3,17 @@ p0 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
 p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
 p0 -> p1;
 
-p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p5 [label="vcf_subfield_title"];
-p1 -> p5 [label="vcf_ch1"];
-
 p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
 p6 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
 p1 -> p6 [label="vcf_ch2"];
 
 p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p23 [label="tsv2vcf"];
-p1 -> p23 [label="vcf_ch3"];
+p5 [label="vcf_subfield_title"];
+p1 -> p5 [label="vcf_ch1"];
+
+p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
+p25 [label="tsv2vcf"];
+p1 -> p25 [label="vcf_ch3"];
 
 p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.from"];
 p6 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
@@ -60,55 +60,63 @@ p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
 p12 -> p13;
 
 p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p23 [label="tsv2vcf"];
-p13 -> p23 [label="fisher_ch4"];
-
-p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p22 [label="miami_plot"];
-p13 -> p22 [label="fisher_ch3"];
+p26 [label="tsv_compress"];
+p13 -> p26 [label="fisher_ch5"];
 
 p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
 p14 [shape=point];
 p13 -> p14 [label="fisher_ch2"];
 
 p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p24 [label="tsv_compress"];
-p13 -> p24 [label="fisher_ch5"];
+p25 [label="tsv2vcf"];
+p13 -> p25 [label="fisher_ch4"];
+
+p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
+p24 [label="miami_plot"];
+p13 -> p24 [label="fisher_ch3"];
 
 p15 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p15 -> p22 [label="chr"];
+p24 [label="miami_plot"];
+p15 -> p24 [label="chr"];
 
 p16 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p16 -> p22 [label="x_lim_val"];
+p24 [label="miami_plot"];
+p16 -> p24 [label="x_lim_val"];
 
 p17 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p17 -> p22 [label="bottom_y_column"];
+p24 [label="miami_plot"];
+p17 -> p24 [label="bottom_y_column"];
 
 p18 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p18 -> p22 [label="color_column"];
+p24 [label="miami_plot"];
+p18 -> p24 [label="color_column"];
 
 p19 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p19 -> p22 [label="y_lim1"];
+p24 [label="miami_plot"];
+p19 -> p24 [label="y_lim1"];
 
 p20 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p20 -> p22 [label="y_lim2"];
+p24 [label="miami_plot"];
+p20 -> p24 [label="y_lim2"];
 
 p21 [shape=point,label="",fixedsize=true,width=0.1];
-p22 [label="miami_plot"];
-p21 -> p22 [label="cute"];
+p24 [label="miami_plot"];
+p21 -> p24 [label="y_log1"];
+
+p22 [shape=point,label="",fixedsize=true,width=0.1];
+p24 [label="miami_plot"];
+p22 -> p24 [label="y_log2"];
+
+p23 [shape=point,label="",fixedsize=true,width=0.1];
+p24 [label="miami_plot"];
+p23 -> p24 [label="cute"];
 
-p25 [shape=point,label="",fixedsize=true,width=0.1];
-p27 [label="Backup"];
-p25 -> p27 [label="config_file"];
+p27 [shape=point,label="",fixedsize=true,width=0.1];
+p29 [label="Backup"];
+p27 -> p29 [label="config_file"];
 
-p26 [shape=point,label="",fixedsize=true,width=0.1];
-p27 [label="Backup"];
-p26 -> p27 [label="log_file"];
+p28 [shape=point,label="",fixedsize=true,width=0.1];
+p29 [label="Backup"];
+p28 -> p29 [label="log_file"];
 
 }
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config b/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config
index 2b510a719d271b19252eff9305e9bd5dd7e86f36..73c3997d10f7538ab298547ce25cff956ba06c40 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config
@@ -28,6 +28,8 @@ env {
     color_column = "NULL" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
     y_lim1 = "NULL" // y-axis limits of the top panel in the miami plot, made of two numbers, separated by a single space. Example: y_lim1 = "0 3". Write "NULL" for no particular limit
     y_lim2 = "NULL" // y-axis limits of the bottom panel in the miami plot, made of two numbers, separated by a single space. Example: y_lim2 = "0 3" .Write "NULL" for no particular limit. Not considered if bottom_y_column = "NULL"
+    y_log1 = "FALSE" // either "TRUE" or "FALSE", y-axis log10 scale for the top panel in the miami plot. Example: y_log1 = "TRUE"
+    y_log2 = "TRUE" // either "TRUE" or "FALSE", y-axis log10 scale for the bottom panel in the miami plot. Example: y_log2 = "TRUE"
     cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 }
 
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt
index 0376b6b24e6cd2c75fe24770c4dd43c94184730e..f2a9d8313f5bd54dc65d0d33da7c4c5d06027dd1 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt
@@ -12,7 +12,7 @@
 
 
 
-2022-11-03 16:09:17
+2022-11-04 15:24:21
 
 
 
@@ -31,7 +31,7 @@
 
 
 
-END TIME: 2022-11-03 16:09:18
+END TIME: 2022-11-04 15:24:23
 
 
 
@@ -64,7 +64,7 @@ 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/Gael/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,AF,NULL,NULL,NULL,cute_little_R_functions.R,miami_report.txt 
+command             /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/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,AF,NULL,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 
@@ -73,6 +73,8 @@ bottom.y.column     AF
 color.column        NULL 
 y.lim1              NULL 
 y.lim2              NULL 
+y.log1              FALSE 
+y.log2              TRUE 
 cute                cute_little_R_functions.R 
 log                 miami_report.txt
 
@@ -99,21 +101,21 @@ locale:
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 
 attached base packages:
-[1] stats     graphics  grDevices utils     datasets  methods   base     
+[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    
+[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       grid_4.1.2       gridExtra_2.3   
-[17] gtable_0.3.0     labeling_0.4.2   lifecycle_1.0.1  magrittr_2.0.2  
-[21] MASS_7.3-55      munsell_0.5.0    pillar_1.7.0     pkgconfig_2.0.3 
-[25] purrr_0.3.4      R6_2.5.1         rlang_1.0.2      scales_1.1.1    
-[29] tibble_3.1.6     tidyselect_1.1.2 utf8_1.2.2       vctrs_0.3.8     
-[33] withr_2.5.0     
+[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     
 
 
 
@@ -121,7 +123,7 @@ loaded via a namespace (and not attached):
 
 ################################ JOB END
 
-TIME: 2022-11-03 16:09:18
+TIME: 2022-11-04 15:24:23
 
 TOTAL TIME LAPSE: 2S
 
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/report.html b/example_of_results/PL_family_WGS_fisher_1667491523/reports/report.html
index 2fda840127467d728aceda5f8da4b2daff598b0e..11b8f753fd3184082e993c3d13f81e9171846fe3 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/report.html
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/report.html
@@ -18,11 +18,11 @@
 <head>
   <meta charset="utf-8">
   <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-  <meta name="description" content="Nextflow workflow report for run id [clever_lamarck]">
+  <meta name="description" content="Nextflow workflow report for run id [loving_bohr]">
   <meta name="author" content="Paolo Di Tommaso, Phil Ewels">
   <link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
 
-  <title>[clever_lamarck] Nextflow Workflow Report</title>
+  <title>[loving_bohr] Nextflow Workflow Report</title>
 
   <style type="text/css">
   /*!
@@ -137,7 +137,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
         <li class="nav-item"><a class="nav-link" href="#tasks">Tasks</a></li>
       </ul>
       <span class="navbar-text">
-        [clever_lamarck]
+        [loving_bohr]
       </span>
     </div>
   </nav>
@@ -146,7 +146,7 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
     <div class="container">
 
       <h1 class="display-3">Nextflow workflow report</h1>
-      <h2 class="text-muted mb-4"><samp>[clever_lamarck]</samp> </h2>
+      <h2 class="text-muted mb-4"><samp>[loving_bohr]</samp> <em>(resumed run)</em></h2>
 
       
           <div class="alert alert-success mb-4">
@@ -157,26 +157,26 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
       <dl>
         <dt>Run times</dt>
         <dd>
-          <span id="workflow_start">03-Nov-2022 17:05:23</span> - <span id="workflow_complete">03-Nov-2022 17:09:19</span>
-          (<span id="completed_fromnow"></span>duration: <strong>3m 55s</strong>)
+          <span id="workflow_start">04-Nov-2022 16:20:49</span> - <span id="workflow_complete">04-Nov-2022 16:24:23</span>
+          (<span id="completed_fromnow"></span>duration: <strong>3m 34s</strong>)
         </dd>
 
         <dl>
           <div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;">
-            <div style="width: 100.0%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="34 tasks succeeded"><span class="text-truncate">&nbsp; 34 succeeded &nbsp;</span></div>
-            <div style="width: 0.0%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="0 tasks were cached"><span class="text-truncate">&nbsp; 0 cached &nbsp;</span></div>
+            <div style="width: 91.18%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="31 tasks succeeded"><span class="text-truncate">&nbsp; 31 succeeded &nbsp;</span></div>
+            <div style="width: 8.82%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="3 tasks were cached"><span class="text-truncate">&nbsp; 3 cached &nbsp;</span></div>
             <div style="width: 0.0%" class="progress-bar bg-warning" data-toggle="tooltip" data-placement="top" title="0 tasks reported and error and were ignored"><span class="text-truncate">&nbsp; 0 ignored &nbsp;</span></div>
             <div style="width: 0.0%" class="progress-bar bg-danger" data-toggle="tooltip" data-placement="top" title="0 tasks failed"><span class="text-truncate">&nbsp; 0 failed &nbsp;</span></div>
           </div>
         </dl>
 
         <dt>Nextflow command</dt>
-        <dd><pre class="nfcommand"><code>nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config</code></pre></dd>
+        <dd><pre class="nfcommand"><code>nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume</code></pre></dd>
       </dl>
 
       <dl class="row small">
         <dt class="col-sm-3">CPU-Hours</dt>
-        <dd class="col-sm-9"><samp>0.1</samp></dd>
+        <dd class="col-sm-9"><samp>0.1 (4.4% cached)</samp></dd>
 
         <dt class="col-sm-3">Launch directory</dt>
         <dd class="col-sm-9"><samp>/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf</samp></dd>
@@ -194,11 +194,11 @@ table.DTCR_clonedTable.dataTable{position:absolute !important;background-color:r
 
         
           <dt class="col-sm-3">Script ID</dt>
-          <dd class="col-sm-9"><code>54ec020277ef1fe7b6c5b3d8c11dfddc</code></dd>
+          <dd class="col-sm-9"><code>4c2737c1211c962f6c61264ad86b50bb</code></dd>
         
 
         <dt class="col-sm-3">Workflow session</dt>
-        <dd class="col-sm-9"><code>c6d68cd5-4752-486f-bad7-d1ec5b02c7df</code></dd>
+        <dd class="col-sm-9"><code>fd98865a-a3cb-4632-b887-6cbb81cfb915</code></dd>
 
         
 
@@ -1029,7 +1029,7 @@ $(function() {
 
   // Nextflow report data
   window.data = { "trace":[
-{"task_id":"3","hash":"e4\/8e01b2","native_id":"21172","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1667491525647","start":"1667491525749","complete":"1667491526289","duration":"642","realtime":"7","%cpu":"20.3","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"155681","wchar":"340","syscr":"252","syscw":"14","read_bytes":"521216","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e4\/8e01b22302fedb5554f9dac70e235e","script":"\n    echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"1","hash":"e0\/1dcdf1","native_id":"21296","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1667491526300","start":"1667491526389","complete":"1667491527257","duration":"957","realtime":"423","%cpu":"19.1","%mem":"0.0","rss":"3649536","vmem":"14155776","peak_rss":"3649536","peak_vmem":"14168064","rchar":"190403","wchar":"1511","syscr":"371","syscw":"35","read_bytes":"4346880","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e0\/1dcdf148b03c417714a4ea37c3fec4","script":"\n    echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n    echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n    echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config\" >> Run_info.txt\n    echo \"execution mode\": local >> Run_info.txt\n    modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n    if [[ ! -z $modules ]] ; then\n        echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\":  >> Run_info.txt\n    fi\n    echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n    echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\" >> Run_info.txt\n    echo \"nextflow version: 21.04.2\" >> Run_info.txt\n    echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n    echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"17","inv_ctxt":"0"},{"task_id":"2","hash":"ef\/c033de","native_id":"21504","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"COMPLETED","exit":"0","submit":"1667491527269","start":"1667491527357","complete":"1667491531008","duration":"3739","realtime":"3261","%cpu":"39.3","%mem":"0.1","rss":"108855296","vmem":"231395328","peak_rss":"108855296","peak_vmem":"231428096","rchar":"12700739","wchar":"3192","syscr":"1666","syscw":"243","read_bytes":"16631808","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/ef\/c033dee6cb23af272c13f4db5ee54c","script":"\n    #!\/bin\/bash -ue\n    vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz \"cute_little_R_functions.R\" \"vcf_subfield_title_report.txt\"\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"16844","inv_ctxt":"12"},{"task_id":"12","hash":"78\/b090f4","native_id":"21844","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (9)","status":"COMPLETED","exit":"0","submit":"1667491531138","start":"1667491531208","complete":"1667491534998","duration":"3860","realtime":"3333","%cpu":"143.9","%mem":"0.1","rss":"135815168","vmem":"1446522880","peak_rss":"135815168","peak_vmem":"1446555648","rchar":"16995114","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52328448","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/78\/b090f4e5c9fb41d75a40d9b83a8106","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr9\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"2976","inv_ctxt":"2"},{"task_id":"6","hash":"36\/11f123","native_id":"22135","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (3)","status":"COMPLETED","exit":"0","submit":"1667491535007","start":"1667491535098","complete":"1667491538728","duration":"3721","realtime":"3223","%cpu":"146.3","%mem":"0.1","rss":"136310784","vmem":"1455468544","peak_rss":"136310784","peak_vmem":"1455501312","rchar":"16995114","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52819968","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/36\/11f123dac0f9b852ca7e98f4f871d8","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr3\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3162","inv_ctxt":"6"},{"task_id":"13","hash":"c2\/063e66","native_id":"22429","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (10)","status":"COMPLETED","exit":"0","submit":"1667491538738","start":"1667491538829","complete":"1667491542488","duration":"3750","realtime":"3284","%cpu":"145.2","%mem":"0.1","rss":"133382144","vmem":"1446522880","peak_rss":"133382144","peak_vmem":"1446555648","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52691968","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c2\/063e66ae0f1e024e8e768a5b614908","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr10\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3014","inv_ctxt":"4"},{"task_id":"5","hash":"72\/11f420","native_id":"22722","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (2)","status":"COMPLETED","exit":"0","submit":"1667491542496","start":"1667491542588","complete":"1667491546158","duration":"3662","realtime":"3173","%cpu":"148.3","%mem":"0.1","rss":"132354048","vmem":"1455730688","peak_rss":"132354048","peak_vmem":"1455763456","rchar":"16995113","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52932608","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/72\/11f420a41fdbd1a1fd15251ddef82d","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr2\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3165","inv_ctxt":"10"},{"task_id":"4","hash":"a1\/6d1200","native_id":"23017","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1667491546166","start":"1667491546258","complete":"1667491666858","duration":"120692","realtime":"120169","%cpu":"57.8","%mem":"0.2","rss":"189104128","vmem":"1512480768","peak_rss":"191393792","peak_vmem":"1514819584","rchar":"17396104","wchar":"13700505","syscr":"2080","syscw":"1951","read_bytes":"53287936","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/a1\/6d120066b74be30c05860fabdd58f4","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"602692","inv_ctxt":"1613"},{"task_id":"16","hash":"9c\/09efe4","native_id":"24878","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (13)","status":"COMPLETED","exit":"0","submit":"1667491666866","start":"1667491666958","complete":"1667491670429","duration":"3563","realtime":"3105","%cpu":"149.9","%mem":"0.1","rss":"140587008","vmem":"1458900992","peak_rss":"140587008","peak_vmem":"1458933760","rchar":"16995114","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52588544","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/9c\/09efe4da75ffc820da318227e7b8ac","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr13\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3267","inv_ctxt":"5"},{"task_id":"17","hash":"b5\/d27919","native_id":"25173","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (14)","status":"COMPLETED","exit":"0","submit":"1667491670436","start":"1667491670529","complete":"1667491673949","duration":"3513","realtime":"3061","%cpu":"152.4","%mem":"0.1","rss":"143163392","vmem":"1458900992","peak_rss":"143163392","peak_vmem":"1458933760","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"51969024","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/b5\/d27919495acd6a5e4df08ef6618da6","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr14\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3242","inv_ctxt":"0"},{"task_id":"15","hash":"b5\/b6744a","native_id":"25466","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (12)","status":"COMPLETED","exit":"0","submit":"1667491673955","start":"1667491674049","complete":"1667491677498","duration":"3543","realtime":"3058","%cpu":"152.3","%mem":"0.1","rss":"142577664","vmem":"1461051392","peak_rss":"142577664","peak_vmem":"1461084160","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52748288","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/b5\/b6744a5fc715b5ddf460e8fb7580b6","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr12\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3349","inv_ctxt":"4"},{"task_id":"14","hash":"78\/e70240","native_id":"25760","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (11)","status":"COMPLETED","exit":"0","submit":"1667491677506","start":"1667491677599","complete":"1667491681169","duration":"3663","realtime":"3192","%cpu":"148.1","%mem":"0.1","rss":"137482240","vmem":"1454919680","peak_rss":"137482240","peak_vmem":"1454952448","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52483072","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/78\/e7024057690dd88ff7beb3383f7353","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr11\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3148","inv_ctxt":"6"},{"task_id":"19","hash":"bc\/4a42c4","native_id":"26055","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (16)","status":"COMPLETED","exit":"0","submit":"1667491681176","start":"1667491681269","complete":"1667491684699","duration":"3523","realtime":"3084","%cpu":"153.7","%mem":"0.1","rss":"142233600","vmem":"1461051392","peak_rss":"142233600","peak_vmem":"1461084160","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52909056","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/bc\/4a42c404177c4da4c612656da3558d","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr16\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3355","inv_ctxt":"12"},{"task_id":"8","hash":"4e\/ee34ed","native_id":"26349","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (5)","status":"COMPLETED","exit":"0","submit":"1667491684706","start":"1667491684799","complete":"1667491688329","duration":"3623","realtime":"3158","%cpu":"148.2","%mem":"0.1","rss":"139771904","vmem":"1456857088","peak_rss":"139771904","peak_vmem":"1456889856","rchar":"16995114","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"53229568","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/4e\/ee34ed10114c04df82f687e3674d99","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr5\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3240","inv_ctxt":"6"},{"task_id":"11","hash":"03\/ea264b","native_id":"26643","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (8)","status":"COMPLETED","exit":"0","submit":"1667491688341","start":"1667491688429","complete":"1667491691839","duration":"3498","realtime":"3084","%cpu":"146.2","%mem":"0.1","rss":"136105984","vmem":"1457176576","peak_rss":"136105984","peak_vmem":"1457209344","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52399104","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/03\/ea264b2a446e935231510dda8d2455","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr8\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3230","inv_ctxt":"12"},{"task_id":"9","hash":"aa\/28aed1","native_id":"26937","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (6)","status":"COMPLETED","exit":"0","submit":"1667491691847","start":"1667491691940","complete":"1667491695450","duration":"3603","realtime":"3156","%cpu":"147.5","%mem":"0.1","rss":"139943936","vmem":"1456857088","peak_rss":"139943936","peak_vmem":"1456889856","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52811776","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/aa\/28aed17f8acb8e78d708c0b8972e76","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr6\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3247","inv_ctxt":"5"},{"task_id":"10","hash":"58\/6fbf6b","native_id":"27229","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (7)","status":"COMPLETED","exit":"0","submit":"1667491695458","start":"1667491695549","complete":"1667491699029","duration":"3571","realtime":"3141","%cpu":"151.9","%mem":"0.1","rss":"139833344","vmem":"1456398336","peak_rss":"139833344","peak_vmem":"1456431104","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52895744","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/58\/6fbf6bb5066302151799a36ca4fee1","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr7\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3231","inv_ctxt":"6"},{"task_id":"7","hash":"b2\/299532","native_id":"27521","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (4)","status":"COMPLETED","exit":"0","submit":"1667491699037","start":"1667491699129","complete":"1667491702609","duration":"3572","realtime":"3084","%cpu":"147.5","%mem":"0.1","rss":"140963840","vmem":"1459609600","peak_rss":"140963840","peak_vmem":"1459642368","rchar":"16995115","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52657152","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/b2\/29953228a2b7379ebdd653a8ade8f1","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr4\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3267","inv_ctxt":"5"},{"task_id":"18","hash":"8a\/a2977e","native_id":"27815","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (15)","status":"COMPLETED","exit":"0","submit":"1667491702616","start":"1667491702710","complete":"1667491706259","duration":"3643","realtime":"3200","%cpu":"147.1","%mem":"0.1","rss":"142147584","vmem":"1460527104","peak_rss":"142147584","peak_vmem":"1460559872","rchar":"16995117","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"53745664","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/8a\/a2977ef03958a2bf1dc2c914e850ee","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr15\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3347","inv_ctxt":"28"},{"task_id":"20","hash":"2e\/4ab4b3","native_id":"28108","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (17)","status":"COMPLETED","exit":"0","submit":"1667491706266","start":"1667491706359","complete":"1667491709809","duration":"3543","realtime":"3079","%cpu":"152.0","%mem":"0.1","rss":"141312000","vmem":"1460068352","peak_rss":"141312000","peak_vmem":"1460101120","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52596736","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/2e\/4ab4b3be8105e81d0219423aa0d375","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr17\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3265","inv_ctxt":"7"},{"task_id":"21","hash":"f7\/e9d070","native_id":"28401","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (18)","status":"COMPLETED","exit":"0","submit":"1667491709817","start":"1667491709909","complete":"1667491713299","duration":"3482","realtime":"3034","%cpu":"153.8","%mem":"0.1","rss":"142340096","vmem":"1461051392","peak_rss":"142340096","peak_vmem":"1461084160","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52590592","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/f7\/e9d0708e9c6371b364a40686bfac26","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr18\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3364","inv_ctxt":"24"},{"task_id":"22","hash":"c1\/58c576","native_id":"28694","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (19)","status":"COMPLETED","exit":"0","submit":"1667491713306","start":"1667491713400","complete":"1667491716868","duration":"3562","realtime":"3141","%cpu":"149.8","%mem":"0.1","rss":"138362880","vmem":"1455730688","peak_rss":"138362880","peak_vmem":"1455763456","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52535296","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c1\/58c57649eb51b07df2be4964cd064e","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr19\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3169","inv_ctxt":"3"},{"task_id":"23","hash":"99\/77a82a","native_id":"28987","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (20)","status":"COMPLETED","exit":"0","submit":"1667491716876","start":"1667491716968","complete":"1667491720499","duration":"3623","realtime":"3112","%cpu":"148.5","%mem":"0.1","rss":"141131776","vmem":"1459609600","peak_rss":"141131776","peak_vmem":"1459642368","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52952064","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/99\/77a82a1a2cbfe94186203cee2939dc","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr20\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3269","inv_ctxt":"8"},{"task_id":"24","hash":"51\/ad7aa4","native_id":"29278","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (21)","status":"COMPLETED","exit":"0","submit":"1667491720506","start":"1667491720599","complete":"1667491724009","duration":"3503","realtime":"3038","%cpu":"152.4","%mem":"0.1","rss":"142643200","vmem":"1461051392","peak_rss":"142643200","peak_vmem":"1461084160","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52311040","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/51\/ad7aa475706510c570c7a5bd042354","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr21\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3352","inv_ctxt":"6"},{"task_id":"25","hash":"e9\/1569b2","native_id":"29570","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (22)","status":"COMPLETED","exit":"0","submit":"1667491724016","start":"1667491724109","complete":"1667491727549","duration":"3533","realtime":"3077","%cpu":"154.0","%mem":"0.1","rss":"141385728","vmem":"1460264960","peak_rss":"141385728","peak_vmem":"1460297728","rchar":"16995117","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52589568","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e9\/1569b2f25edd798f0aaad8998e898f","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr22\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3278","inv_ctxt":"6"},{"task_id":"26","hash":"ad\/121fd1","native_id":"29863","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (23)","status":"COMPLETED","exit":"0","submit":"1667491727555","start":"1667491727649","complete":"1667491731049","duration":"3494","realtime":"3008","%cpu":"156.8","%mem":"0.1","rss":"145555456","vmem":"1467904000","peak_rss":"145555456","peak_vmem":"1467936768","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"53168128","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/ad\/121fd118cd8cb843dd48a27810eb1d","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr23\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3484","inv_ctxt":"4"},{"task_id":"27","hash":"c9\/8f6265","native_id":"30156","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (24)","status":"COMPLETED","exit":"0","submit":"1667491731055","start":"1667491731149","complete":"1667491734699","duration":"3644","realtime":"3121","%cpu":"149.9","%mem":"0.1","rss":"141434880","vmem":"1460068352","peak_rss":"141434880","peak_vmem":"1460101120","rchar":"16995117","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"53256192","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c9\/8f626583cdc894c6859a80bf6079c2","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr24\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3300","inv_ctxt":"7"},{"task_id":"28","hash":"1d\/564b3c","native_id":"30449","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (25)","status":"COMPLETED","exit":"0","submit":"1667491734706","start":"1667491734799","complete":"1667491738279","duration":"3573","realtime":"3093","%cpu":"149.8","%mem":"0.1","rss":"139354112","vmem":"1460264960","peak_rss":"139354112","peak_vmem":"1460297728","rchar":"16995117","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52796416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/1d\/564b3cba09b279d0ca394177dbcfe4","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr25\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3295","inv_ctxt":"13"},{"task_id":"29","hash":"a9\/db74b8","native_id":"30742","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (26)","status":"COMPLETED","exit":"0","submit":"1667491738286","start":"1667491738379","complete":"1667491742000","duration":"3714","realtime":"3238","%cpu":"147.4","%mem":"0.1","rss":"135585792","vmem":"1451134976","peak_rss":"135585792","peak_vmem":"1451167744","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52700160","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/a9\/db74b8be98b4e5a6764ae9fd16652c","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chrY\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3097","inv_ctxt":"16"},{"task_id":"30","hash":"4e\/44a80d","native_id":"31036","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (27)","status":"COMPLETED","exit":"0","submit":"1667491742008","start":"1667491742100","complete":"1667491745749","duration":"3741","realtime":"3278","%cpu":"143.9","%mem":"0.1","rss":"137285632","vmem":"1454919680","peak_rss":"137285632","peak_vmem":"1454952448","rchar":"16995117","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52646912","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/4e\/44a80d2f790a483a40eef5d3462dc7","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chrX\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3125","inv_ctxt":"22"},{"task_id":"31","hash":"52\/e45ccb","native_id":"31329","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (28)","status":"COMPLETED","exit":"0","submit":"1667491745756","start":"1667491745849","complete":"1667491749439","duration":"3683","realtime":"3190","%cpu":"147.2","%mem":"0.1","rss":"141582336","vmem":"1460264960","peak_rss":"141582336","peak_vmem":"1460297728","rchar":"16995116","wchar":"648","syscr":"2024","syscw":"14","read_bytes":"52754432","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/52\/e45ccb8292b0bb513b5084405f4448","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chrM\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3272","inv_ctxt":"54"},{"task_id":"33","hash":"7c\/11086c","native_id":"31632","process":"tsv_compress","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv_compress (1)","status":"COMPLETED","exit":"0","submit":"1667491750252","start":"1667491750340","complete":"1667491751129","duration":"877","realtime":"381","%cpu":"66.8","%mem":"0.0","rss":"5308416","vmem":"10412032","peak_rss":"5308416","peak_vmem":"10436608","rchar":"13859990","wchar":"1196543","syscr":"683","syscw":"17","read_bytes":"580608","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/7c\/11086c8cc31aa55851279828f2c2ef","script":"\n    #!\/bin\/bash -ue\n    gzip -cf9 fisher.tsv > res_fisher.tsv.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667491523\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"112","inv_ctxt":"3"},{"task_id":"34","hash":"39\/b87f10","native_id":"31782","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1667491751135","start":"1667491751229","complete":"1667491754539","duration":"3404","realtime":"2869","%cpu":"34.0","%mem":"0.0","rss":"7835648","vmem":"18702336","peak_rss":"7835648","peak_vmem":"18735104","rchar":"29503927","wchar":"15355206","syscr":"2676","syscw":"18425","read_bytes":"1334272","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/39\/b87f1024f81aefb13204a4711cc1df","script":"\n    #!\/bin\/bash -ue\n    PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n    HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n    echo -e $PREHEADER > res_fisher.vcf\n    FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\") # recover a file name without path\n    FILE_EXTENSION=\"${FILENAME##*.}\" #  ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n    if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n        zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz | awk \'{\n            if($0 ~ \"^##.*\"){\n                print $0\n            }else{\n                exit 0\n            }\n        }\' >> res_fisher.vcf\n    else\n        awk \'{\n            if($0 ~ \"^##.*\"){\n                print $0\n            }else{\n                exit 0\n            }\n        }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz >> res_fisher.vcf\n    fi\n    awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n        NR==1{\n            print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n            print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n            print \"##INFO=<ID=FISHER,Number=.,Type=String,Description=\"\"Fisher exact tests based on the presence\/absence of the variant in the affected\/unaffected indiv. Format: \" ;\n            for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n            print \"\"\">\\n\" ;\n            print var1\"\\n\"\n        }\n        NR > 1{\n            gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n            print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n            for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n            print \"\\n\"\n        }\n    \' fisher.tsv >> res_fisher.vcf\n    bgzip -f -l 9 res_fisher.vcf > res_fisher.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n    tabix -p vcf res_fisher.vcf.gz # htslib command\n    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chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM\" \"AF\" \"NULL\" \"NULL\" \"NULL\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT 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(1)"},"time":{"mean":4284,"min":4284,"q1":4284,"q2":4284,"q3":4284,"max":4284,"minLabel":"miami_plot (1)","maxLabel":"miami_plot (1)","q1Label":"miami_plot (1)","q2Label":"miami_plot (1)","q3Label":"miami_plot (1)"},"writes":{"mean":52561,"min":52561,"q1":52561,"q2":52561,"q3":52561,"max":52561,"minLabel":"miami_plot (1)","maxLabel":"miami_plot (1)","q1Label":"miami_plot (1)","q2Label":"miami_plot (1)","q3Label":"miami_plot (1)"}}] };
+{"task_id":"1","hash":"99\/439dda","native_id":"13012","process":"WorkflowVersion","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"WorkflowVersion","status":"COMPLETED","exit":"0","submit":"1667575251403","start":"1667575251448","complete":"1667575252472","duration":"1069","realtime":"453","%cpu":"17.9","%mem":"0.0","rss":"3788800","vmem":"14155776","peak_rss":"3788800","peak_vmem":"14168064","rchar":"190390","wchar":"1517","syscr":"373","syscw":"35","read_bytes":"4717568","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/99\/439dda5d11dfe9e9b04557807a3918","script":"\n    echo \"Project (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf remote -v | head -n 1) > Run_info.txt # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo\n    echo \"Git info (empty means no .git folder where the main.nf file is present): \" $(git -C \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf describe --abbrev=10 --dirty --always --tags) >> Run_info.txt # idem. Provide the small commit number of the script and nextflow.config used in the execution\n    echo \"Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume\" >> Run_info.txt\n    echo \"execution mode\": local >> Run_info.txt\n    modules= # this is just to deal with variable interpretation during the creation of the .command.sh file by nextflow. See also $modules below\n    if [[ ! -z $modules ]] ; then\n        echo \"loaded modules (according to specification by the user thanks to the --modules argument of main.nf)\":  >> Run_info.txt\n    fi\n    echo \"Manifest\'s pipeline version: null\" >> Run_info.txt\n    echo \"result path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\" >> Run_info.txt\n    echo \"nextflow version: 21.04.2\" >> Run_info.txt\n    echo -e \"\\n\\nIMPLICIT VARIABLES:\\n\\nlaunchDir (directory where the workflow is run): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nprojectDir (directory where the main.nf script is located): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nworkDir (directory where tasks temporary files are created): \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\" >> Run_info.txt\n    echo -e \"\\n\\nUSER VARIABLES:\\n\\nout_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\\nsample_path: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\" >> Run_info.txt\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"17","inv_ctxt":"0"},{"task_id":"2","hash":"3b\/d18102","native_id":"11839","process":"vcf_subfield_title","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"vcf_subfield_title (1)","status":"CACHED","exit":"0","submit":"1667575231579","start":"1667575231670","complete":"1667575235042","duration":"3463","realtime":"2998","%cpu":"40.4","%mem":"0.1","rss":"108081152","vmem":"230539264","peak_rss":"108081152","peak_vmem":"230572032","rchar":"12700654","wchar":"3189","syscr":"1666","syscw":"243","read_bytes":"16881664","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/3b\/d181022684ca6b11126107d12c1679","script":"\n    #!\/bin\/bash -ue\n    vcf_subfield_title.R Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz \"cute_little_R_functions.R\" \"vcf_subfield_title_report.txt\"\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575228\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"10567","inv_ctxt":"3"},{"task_id":"5","hash":"17\/0f9148","native_id":"12124","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (2)","status":"CACHED","exit":"0","submit":"1667575235143","start":"1667575235241","complete":"1667575238662","duration":"3519","realtime":"3031","%cpu":"154.2","%mem":"0.1","rss":"143253504","vmem":"1461825536","peak_rss":"143253504","peak_vmem":"1461858304","rchar":"16995031","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"53086208","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/17\/0f9148538be962ccb9098d2f55c8c3","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr2\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575228\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3385","inv_ctxt":"54"},{"task_id":"19","hash":"28\/827bd6","native_id":"12413","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (13)","status":"CACHED","exit":"0","submit":"1667575238669","start":"1667575238762","complete":"1667575242131","duration":"3462","realtime":"2966","%cpu":"157.0","%mem":"0.1","rss":"143458304","vmem":"1462190080","peak_rss":"143458304","peak_vmem":"1462222848","rchar":"16995032","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52905984","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/28\/827bd66627f7b4e39b915cd5f58cb5","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr13\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575228\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3399","inv_ctxt":"6"},{"task_id":"3","hash":"9a\/5b654f","native_id":"13233","process":"Backup","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"Backup","status":"COMPLETED","exit":"0","submit":"1667575252485","start":"1667575252572","complete":"1667575253021","duration":"536","realtime":"6","%cpu":"20.0","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"155603","wchar":"338","syscr":"252","syscw":"14","read_bytes":"521216","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/9a\/5b654f66666ddc89a01231950980b1","script":"\n    echo -e \"full .nextflow.log is in: \/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\\nThe one in the result folder is not complete (miss the end)\" > Log_info.txt\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"0","inv_ctxt":"0"},{"task_id":"6","hash":"52\/2c38de","native_id":"13359","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (3)","status":"COMPLETED","exit":"0","submit":"1667575253030","start":"1667575253121","complete":"1667575256502","duration":"3472","realtime":"3011","%cpu":"155.5","%mem":"0.1","rss":"142557184","vmem":"1461301248","peak_rss":"142557184","peak_vmem":"1461334016","rchar":"16995038","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52641792","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/52\/2c38de57856faece561ff861f7b5c7","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr3\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3357","inv_ctxt":"3"},{"task_id":"8","hash":"55\/559994","native_id":"13649","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (5)","status":"COMPLETED","exit":"0","submit":"1667575256510","start":"1667575256602","complete":"1667575259971","duration":"3461","realtime":"3029","%cpu":"153.6","%mem":"0.1","rss":"141430784","vmem":"1460264960","peak_rss":"141430784","peak_vmem":"1460297728","rchar":"16995042","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52325376","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/55\/5599942a95bde63e934f0426fff51a","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr5\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3293","inv_ctxt":"17"},{"task_id":"7","hash":"dc\/c2eab9","native_id":"13942","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (4)","status":"COMPLETED","exit":"0","submit":"1667575259980","start":"1667575260071","complete":"1667575263472","duration":"3492","realtime":"2992","%cpu":"155.7","%mem":"0.1","rss":"142471168","vmem":"1461563392","peak_rss":"142471168","peak_vmem":"1461596160","rchar":"16995041","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52520960","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/dc\/c2eab9ddf107793e0dd980455fec5b","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr4\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3376","inv_ctxt":"2"},{"task_id":"13","hash":"1e\/fd5994","native_id":"14234","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (10)","status":"COMPLETED","exit":"0","submit":"1667575263482","start":"1667575263572","complete":"1667575267071","duration":"3589","realtime":"3102","%cpu":"149.3","%mem":"0.1","rss":"139599872","vmem":"1456136192","peak_rss":"139599872","peak_vmem":"1456168960","rchar":"16995045","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52769792","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/1e\/fd5994d2ab5780944a71387a45f2af","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr10\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3226","inv_ctxt":"10"},{"task_id":"10","hash":"7d\/48d1cf","native_id":"14527","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (7)","status":"COMPLETED","exit":"0","submit":"1667575267079","start":"1667575267171","complete":"1667575270672","duration":"3593","realtime":"3168","%cpu":"144.6","%mem":"0.1","rss":"137728000","vmem":"1454919680","peak_rss":"137728000","peak_vmem":"1454952448","rchar":"16995047","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52704256","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/7d\/48d1cf69b659a4ec84bc4d575f4ab1","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr7\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3133","inv_ctxt":"3"},{"task_id":"12","hash":"94\/ea5f77","native_id":"14820","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (9)","status":"COMPLETED","exit":"0","submit":"1667575270679","start":"1667575270772","complete":"1667575274172","duration":"3493","realtime":"3055","%cpu":"153.9","%mem":"0.1","rss":"142573568","vmem":"1461051392","peak_rss":"142573568","peak_vmem":"1461084160","rchar":"16995048","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52718592","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/94\/ea5f77542bdce3479f8a32bdedc61e","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr9\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3353","inv_ctxt":"9"},{"task_id":"9","hash":"72\/779535","native_id":"15114","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (6)","status":"COMPLETED","exit":"0","submit":"1667575274179","start":"1667575274272","complete":"1667575277681","duration":"3502","realtime":"3041","%cpu":"155.1","%mem":"0.1","rss":"142852096","vmem":"1461563392","peak_rss":"142852096","peak_vmem":"1461596160","rchar":"16995048","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52738048","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/72\/779535cf74ba850fc4a38686499abb","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr6\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3375","inv_ctxt":"6"},{"task_id":"11","hash":"d9\/7e2d0e","native_id":"15409","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (8)","status":"COMPLETED","exit":"0","submit":"1667575277688","start":"1667575277781","complete":"1667575281131","duration":"3443","realtime":"2993","%cpu":"154.6","%mem":"0.1","rss":"142422016","vmem":"1461563392","peak_rss":"142422016","peak_vmem":"1461596160","rchar":"16995048","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52272128","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/d9\/7e2d0e9054e568bafeccfcd56fe0e4","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr8\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3346","inv_ctxt":"29"},{"task_id":"17","hash":"06\/09f270","native_id":"15703","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (13)","status":"COMPLETED","exit":"0","submit":"1667575281138","start":"1667575281232","complete":"1667575284662","duration":"3524","realtime":"3083","%cpu":"149.8","%mem":"0.1","rss":"142086144","vmem":"1460789248","peak_rss":"142086144","peak_vmem":"1460822016","rchar":"16995051","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"53046272","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/06\/09f27084a96e3a4e2454720f5e394a","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr15\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3341","inv_ctxt":"3"},{"task_id":"16","hash":"7b\/1bf59a","native_id":"15996","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (14)","status":"COMPLETED","exit":"0","submit":"1667575284669","start":"1667575284762","complete":"1667575288181","duration":"3512","realtime":"3054","%cpu":"151.1","%mem":"0.1","rss":"146235392","vmem":"1460527104","peak_rss":"146235392","peak_vmem":"1460559872","rchar":"16995053","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52702208","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/7b\/1bf59a996b2dca06a4405228063efe","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr16\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3304","inv_ctxt":"2"},{"task_id":"4","hash":"10\/61ad6f","native_id":"16289","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (1)","status":"COMPLETED","exit":"0","submit":"1667575288189","start":"1667575288281","complete":"1667575401942","duration":"113753","realtime":"113328","%cpu":"56.7","%mem":"0.2","rss":"184348672","vmem":"1511702528","peak_rss":"187424768","peak_vmem":"1514987520","rchar":"17396048","wchar":"13700503","syscr":"2080","syscw":"1951","read_bytes":"52849664","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/10\/61ad6fe5082c9e41d3bc137ef2a566","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr1\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"610982","inv_ctxt":"1692"},{"task_id":"18","hash":"fa\/658eee","native_id":"18094","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (15)","status":"COMPLETED","exit":"0","submit":"1667575401951","start":"1667575402041","complete":"1667575405411","duration":"3460","realtime":"3005","%cpu":"153.1","%mem":"0.1","rss":"142884864","vmem":"1461563392","peak_rss":"142884864","peak_vmem":"1461596160","rchar":"16995060","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52486144","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/fa\/658eee81ad6db09e953d09bf3a55fe","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr14\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3374","inv_ctxt":"7"},{"task_id":"14","hash":"a8\/0a235c","native_id":"18388","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (11)","status":"COMPLETED","exit":"0","submit":"1667575405419","start":"1667575405511","complete":"1667575408911","duration":"3492","realtime":"3003","%cpu":"156.0","%mem":"0.1","rss":"141803520","vmem":"1460527104","peak_rss":"141803520","peak_vmem":"1460559872","rchar":"16995061","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52413440","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/a8\/0a235c6158b4e7513b8a4f257b8fa8","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr11\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3300","inv_ctxt":"2"},{"task_id":"15","hash":"ee\/dd0f79","native_id":"18682","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (12)","status":"COMPLETED","exit":"0","submit":"1667575408920","start":"1667575409011","complete":"1667575412382","duration":"3462","realtime":"3020","%cpu":"155.3","%mem":"0.1","rss":"142393344","vmem":"1461051392","peak_rss":"142393344","peak_vmem":"1461084160","rchar":"16995063","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52619264","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/ee\/dd0f797e105dcdfcde58d6e142f307","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr12\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3360","inv_ctxt":"3"},{"task_id":"20","hash":"73\/b515a9","native_id":"18975","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (17)","status":"COMPLETED","exit":"0","submit":"1667575412390","start":"1667575412481","complete":"1667575415872","duration":"3482","realtime":"2996","%cpu":"156.3","%mem":"0.1","rss":"142229504","vmem":"1461563392","peak_rss":"142229504","peak_vmem":"1461596160","rchar":"16995063","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52579328","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/73\/b515a90ba6425409a84eac93679e93","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr17\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3364","inv_ctxt":"3"},{"task_id":"21","hash":"05\/3831aa","native_id":"19268","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (18)","status":"COMPLETED","exit":"0","submit":"1667575415891","start":"1667575415972","complete":"1667575419421","duration":"3530","realtime":"3092","%cpu":"149.1","%mem":"0.1","rss":"142196736","vmem":"1460789248","peak_rss":"142196736","peak_vmem":"1460822016","rchar":"16995066","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"53105664","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/05\/3831aaeeee757bcf23d16b7e1498b9","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr18\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3366","inv_ctxt":"24"},{"task_id":"22","hash":"94\/c16c25","native_id":"19561","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (19)","status":"COMPLETED","exit":"0","submit":"1667575419429","start":"1667575419521","complete":"1667575423002","duration":"3573","realtime":"3092","%cpu":"150.7","%mem":"0.1","rss":"142086144","vmem":"1460789248","peak_rss":"142086144","peak_vmem":"1460822016","rchar":"16995068","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"53195776","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/94\/c16c25e5ae17160ed1f3b5fd403a26","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr19\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3346","inv_ctxt":"27"},{"task_id":"23","hash":"2b\/a27946","native_id":"19855","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (20)","status":"COMPLETED","exit":"0","submit":"1667575423009","start":"1667575423102","complete":"1667575426502","duration":"3493","realtime":"3032","%cpu":"153.3","%mem":"0.1","rss":"143265792","vmem":"1461825536","peak_rss":"143265792","peak_vmem":"1461858304","rchar":"16995069","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52854784","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/2b\/a27946fb12dc8bb25e19eb355fef4c","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr20\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3386","inv_ctxt":"6"},{"task_id":"25","hash":"29\/3f925b","native_id":"20148","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (22)","status":"COMPLETED","exit":"0","submit":"1667575426509","start":"1667575426602","complete":"1667575429991","duration":"3482","realtime":"3021","%cpu":"154.4","%mem":"0.1","rss":"142528512","vmem":"1461051392","peak_rss":"142528512","peak_vmem":"1461084160","rchar":"16995076","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52998144","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/29\/3f925b86916b6b1bb5a0bb9adec02b","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr22\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3368","inv_ctxt":"3"},{"task_id":"24","hash":"85\/8c0cf7","native_id":"20440","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (21)","status":"COMPLETED","exit":"0","submit":"1667575429999","start":"1667575430092","complete":"1667575433541","duration":"3542","realtime":"3088","%cpu":"150.7","%mem":"0.1","rss":"142815232","vmem":"1461051392","peak_rss":"142815232","peak_vmem":"1461084160","rchar":"16995076","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52977664","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/85\/8c0cf783af32d3ca6975612a71d454","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr21\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3361","inv_ctxt":"5"},{"task_id":"26","hash":"91\/bdc450","native_id":"20733","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (23)","status":"COMPLETED","exit":"0","submit":"1667575433548","start":"1667575433642","complete":"1667575437091","duration":"3543","realtime":"3045","%cpu":"154.0","%mem":"0.1","rss":"141938688","vmem":"1460527104","peak_rss":"141938688","peak_vmem":"1460559872","rchar":"16995078","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52654080","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/91\/bdc450cd99f853792c152be55f5a38","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr23\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3294","inv_ctxt":"5"},{"task_id":"27","hash":"e1\/be1d29","native_id":"21026","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (24)","status":"COMPLETED","exit":"0","submit":"1667575437097","start":"1667575437192","complete":"1667575440552","duration":"3455","realtime":"3010","%cpu":"152.8","%mem":"0.1","rss":"142528512","vmem":"1461563392","peak_rss":"142528512","peak_vmem":"1461596160","rchar":"16995078","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52780032","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e1\/be1d2951b060ee4ef4c7e175cb7857","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr24\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3365","inv_ctxt":"2"},{"task_id":"28","hash":"68\/3f0978","native_id":"21319","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (25)","status":"COMPLETED","exit":"0","submit":"1667575440559","start":"1667575440651","complete":"1667575444011","duration":"3452","realtime":"3002","%cpu":"155.1","%mem":"0.1","rss":"142577664","vmem":"1461563392","peak_rss":"142577664","peak_vmem":"1461596160","rchar":"16995079","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52730880","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/68\/3f097867fa9f0bd0ee83badb2955a5","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chr25\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3383","inv_ctxt":"6"},{"task_id":"29","hash":"84\/3dec27","native_id":"21612","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (26)","status":"COMPLETED","exit":"0","submit":"1667575444018","start":"1667575444112","complete":"1667575447402","duration":"3384","realtime":"2974","%cpu":"156.8","%mem":"0.1","rss":"142491648","vmem":"1461051392","peak_rss":"142491648","peak_vmem":"1461084160","rchar":"16995078","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52450304","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/84\/3dec274bc7fa538dc995a3fc1e68f6","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chrY\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3343","inv_ctxt":"4"},{"task_id":"30","hash":"47\/88cf99","native_id":"21905","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (27)","status":"COMPLETED","exit":"0","submit":"1667575447408","start":"1667575447502","complete":"1667575450921","duration":"3513","realtime":"3005","%cpu":"155.2","%mem":"0.1","rss":"142659584","vmem":"1461563392","peak_rss":"142659584","peak_vmem":"1461596160","rchar":"16995078","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52868096","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/47\/88cf9962ffb2f1eff058bae64a1ba0","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chrX\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3375","inv_ctxt":"4"},{"task_id":"31","hash":"94\/f91af0","native_id":"22198","process":"fisher","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-python_v3.9.10_extended_v3.1-gitlab_v8.7.img","tag":"-","name":"fisher (28)","status":"COMPLETED","exit":"0","submit":"1667575450928","start":"1667575451021","complete":"1667575454312","duration":"3384","realtime":"2942","%cpu":"157.8","%mem":"0.1","rss":"143876096","vmem":"1463840768","peak_rss":"143876096","peak_vmem":"1463873536","rchar":"16995079","wchar":"646","syscr":"2024","syscw":"14","read_bytes":"52788224","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/94\/f91af0f280fc2faae9c69043c678b6","script":"\n    #!\/bin\/bash -ue\n    if grep -Eq \"FISHER\" vcf_info_field_titles.txt ; then # does not work without [[]]\n        echo -e \"\\n\\n========\\n\\nERROR IN NEXTFLOW EXECUTION\\n\\nTHE VCF FILE HAS ALREADY FISHER COMPUTATION PERFORMED, AS FIELDS ARE:\\n$(cat vcf_info_field_titles.txt)\\n\\n========\\n\\n\"\n        exit 1\n    else\n        fisher_lod.py Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz Dyslexia.pedigree.txt \"chrM\" vcf_info_field_titles.txt \"AC AF CSQ_SIFT CSQ_PolyPhen\" vcf_csq_subfield_titles.txt \"fisher_report.txt\"\n    fi\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3426","inv_ctxt":"10"},{"task_id":"33","hash":"5c\/3c2a26","native_id":"22501","process":"tsv_compress","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv_compress (1)","status":"COMPLETED","exit":"0","submit":"1667575455084","start":"1667575455113","complete":"1667575455881","duration":"797","realtime":"353","%cpu":"67.5","%mem":"0.0","rss":"5206016","vmem":"10412032","peak_rss":"5206016","peak_vmem":"10436608","rchar":"13859953","wchar":"1196541","syscr":"683","syscw":"17","read_bytes":"580608","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/5c\/3c2a26848986af4fcd26939252b88f","script":"\n    #!\/bin\/bash -ue\n    gzip -cf9 fisher.tsv > res_fisher.tsv.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"107","inv_ctxt":"1"},{"task_id":"34","hash":"f0\/b2c43f","native_id":"22649","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv2vcf (1)","status":"COMPLETED","exit":"0","submit":"1667575455888","start":"1667575455981","complete":"1667575458891","duration":"3003","realtime":"2513","%cpu":"31.7","%mem":"0.0","rss":"7741440","vmem":"18706432","peak_rss":"7741440","peak_vmem":"18739200","rchar":"29503889","wchar":"15355203","syscr":"2676","syscw":"18425","read_bytes":"1340416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/f0\/b2c43fa1bebba69f0445319a9bfc08","script":"\n    #!\/bin\/bash -ue\n    PREHEADER=\'##fileformat=VCFv4.2;build by fisher_for_vcf.nf\\n##WARNING: This file is not a true VCF since FORMAT AND sample (indiv) columns are not present\'\n    HEADER=\'#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\'\n    echo -e $PREHEADER > res_fisher.vcf\n    FILENAME=$(basename -- \"Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\") # recover a file name without path\n    FILE_EXTENSION=\"${FILENAME##*.}\" #  ## means \"delete the longest regex starting at the beginning of the tested string\". If nothing, delete nothing. Thus ##*. means delete the longest string finishing by a dot. Use # instead of ## for \"delete the shortest regex starting at the beginning of the tested string\"\n    if [[ \"${FILE_EXTENSION}\" =~ gz ]] ; then\n        zcat Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz | awk \'{\n            if($0 ~ \"^##.*\"){\n                print $0\n            }else{\n                exit 0\n            }\n        }\' >> res_fisher.vcf\n    else\n        awk \'{\n            if($0 ~ \"^##.*\"){\n                print $0\n            }else{\n                exit 0\n            }\n        }\' Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz >> res_fisher.vcf\n    fi\n    awk -v var1=$HEADER \'BEGIN{FS=\"\\t\" ; OFS=\"\" ; ORS=\"\"}\n        NR==1{\n            print \"##WARNING: 5 first names of the header of the initial file: \"$1\" \"$2\" \"$3\" \"$4\" \"$5\"\\n\" ;\n            print \"##WARNING: if the 5 first columns of the .tsv file are not CHROM POS REF ALT INFO, then the .vcf file produced by this process is not good\\n\" ;\n            print \"##INFO=<ID=FISHER,Number=.,Type=String,Description=\"\"Fisher exact tests based on the presence\/absence of the variant in the affected\/unaffected indiv. Format: \" ;\n            for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n            print \"\"\">\\n\" ;\n            print var1\"\\n\"\n        }\n        NR > 1{\n            gsub(\"[\\\\[\\\\]\\\'\"\'\"\']\", \"\", $4)\n            print $1\"\\t\"$2\"\\t.\\t\"$3\"\\t\"$4\"\\t.\\t.\\t\"$5\";FISHER=\" ;\n            for(i=6;i<=NF;i++){print $i ; if(i < NF){print \"|\"}} ;\n            print \"\\n\"\n        }\n    \' fisher.tsv >> res_fisher.vcf\n    bgzip -f -l 9 res_fisher.vcf > res_fisher.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n    tabix -p vcf res_fisher.vcf.gz # htslib command\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"9824","inv_ctxt":"2"},{"task_id":"32","hash":"9a\/ba59a6","native_id":"22913","process":"miami_plot","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-r_v4.1.2_extended_v2.1-gitlab_v8.8.img","tag":"-","name":"miami_plot (1)","status":"COMPLETED","exit":"0","submit":"1667575458897","start":"1667575458991","complete":"1667575463661","duration":"4764","realtime":"4278","%cpu":"63.4","%mem":"0.2","rss":"184590336","vmem":"327589888","peak_rss":"186241024","peak_vmem":"329007104","rchar":"28617187","wchar":"61871","syscr":"5964","syscw":"227","read_bytes":"42109952","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/9a\/ba59a69b618b472c6e76eb6e9f3afa","script":"\n    #!\/bin\/bash -ue\n    miami.R 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\" \"AF\" \"NULL\" \"NULL\" \"NULL\" \"FALSE\" \"TRUE\" \"cute_little_R_functions.R\" \"miami_report.txt\"\n    ","scratch":"-","queue":"-","cpus":"1","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=whole\nbottom_y_column=AF\ncolor_column=NULL\ny_lim1=NULL\ny_lim2=NULL\ny_log1=FALSE\ny_log2=TRUE\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1667575249\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"6629","inv_ctxt":"13"}], "summary":[{"cpuUsage":{"mean":40.4,"min":40.4,"q1":40.4,"q2":40.4,"q3":40.4,"max":40.4,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"process":"vcf_subfield_title","mem":{"mean":108081152,"min":108081152,"q1":108081152,"q2":108081152,"q3":108081152,"max":108081152,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"memUsage":{"mean":0.16,"min":0.16,"q1":0.16,"q2":0.16,"q3":0.16,"max":0.16,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"timeUsage":null,"vmem":{"mean":230572032,"min":230572032,"q1":230572032,"q2":230572032,"q3":230572032,"max":230572032,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"reads":{"mean":12700654,"min":12700654,"q1":12700654,"q2":12700654,"q3":12700654,"max":12700654,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"cpu":{"mean":40.4,"min":40.4,"q1":40.4,"q2":40.4,"q3":40.4,"max":40.4,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"time":{"mean":2998,"min":2998,"q1":2998,"q2":2998,"q3":2998,"max":2998,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"},"writes":{"mean":3189,"min":3189,"q1":3189,"q2":3189,"q3":3189,"max":3189,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title (1)"}},{"cpuUsage":{"mean":150.06,"min":56.7,"q1":151,"q2":154.1,"q3":155.35,"max":157.8,"minLabel":"fisher 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diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html b/example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html
index 12188039a20a5f076a6f5b8f201be19ab31f7491..74f13f2a14780644d2f4aa24b4a27ef1c9632dc6 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html
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-        {"label": "tsv2vcf (1)", "cached": false, "index": 5, "times": [{"starting_time": 1667491751135, "ending_time": 1667491751229}, {"starting_time": 1667491751229, "ending_time": 1667491754098, "label": "3.4s \/ 7.5 MB"}, {"starting_time": 1667491754098, "ending_time": 1667491754539}]},
-        {"label": "miami_plot (1)", "cached": false, "index": 6, "times": [{"starting_time": 1667491754545, "ending_time": 1667491754639}, {"starting_time": 1667491754639, "ending_time": 1667491758923, "label": "4.7s \/ 182.1 MB"}, {"starting_time": 1667491758923, "ending_time": 1667491759259}]}
+        {"label": "WorkflowVersion", "cached": false, "index": 0, "times": [{"starting_time": 1667575251403, "ending_time": 1667575251448}, {"starting_time": 1667575251448, "ending_time": 1667575251901, "label": "1.1s \/ 3.6 MB"}, {"starting_time": 1667575251901, "ending_time": 1667575252472}]},
+        {"label": "vcf_subfield_title (1)", "cached": true, "index": 1, "times": [{"starting_time": 1667575231579, "ending_time": 1667575231670}, {"starting_time": 1667575231670, "ending_time": 1667575234668, "label": "3.5s \/ 103.1 MB \/ CACHED"}, {"starting_time": 1667575234668, "ending_time": 1667575235042}]},
+        {"label": "fisher (2)", "cached": true, "index": 2, "times": [{"starting_time": 1667575235143, "ending_time": 1667575235241}, {"starting_time": 1667575235241, "ending_time": 1667575238272, "label": "3.5s \/ 136.6 MB \/ CACHED"}, {"starting_time": 1667575238272, "ending_time": 1667575238662}]},
+        {"label": "fisher (13)", "cached": true, "index": 2, "times": [{"starting_time": 1667575238669, "ending_time": 1667575238762}, {"starting_time": 1667575238762, "ending_time": 1667575241728, "label": "3.5s \/ 136.8 MB \/ CACHED"}, {"starting_time": 1667575241728, "ending_time": 1667575242131}]},
+        {"label": "Backup", "cached": false, "index": 3, "times": [{"starting_time": 1667575252485, "ending_time": 1667575252572}, {"starting_time": 1667575252572, "ending_time": 1667575252578, "label": "536ms \/ 0"}, {"starting_time": 1667575252578, "ending_time": 1667575253021}]},
+        {"label": "fisher (3)", "cached": false, "index": 2, "times": [{"starting_time": 1667575253030, "ending_time": 1667575253121}, {"starting_time": 1667575253121, "ending_time": 1667575256132, "label": "3.5s \/ 136 MB"}, {"starting_time": 1667575256132, "ending_time": 1667575256502}]},
+        {"label": "fisher (5)", "cached": false, "index": 2, "times": [{"starting_time": 1667575256510, "ending_time": 1667575256602}, {"starting_time": 1667575256602, "ending_time": 1667575259631, "label": "3.5s \/ 134.9 MB"}, {"starting_time": 1667575259631, "ending_time": 1667575259971}]},
+        {"label": "fisher (4)", "cached": false, "index": 2, "times": [{"starting_time": 1667575259980, "ending_time": 1667575260071}, {"starting_time": 1667575260071, "ending_time": 1667575263063, "label": "3.5s \/ 135.9 MB"}, {"starting_time": 1667575263063, "ending_time": 1667575263472}]},
+        {"label": "fisher (10)", "cached": false, "index": 2, "times": [{"starting_time": 1667575263482, "ending_time": 1667575263572}, {"starting_time": 1667575263572, "ending_time": 1667575266674, "label": "3.6s \/ 133.1 MB"}, {"starting_time": 1667575266674, "ending_time": 1667575267071}]},
+        {"label": "fisher (7)", "cached": false, "index": 2, "times": [{"starting_time": 1667575267079, "ending_time": 1667575267171}, {"starting_time": 1667575267171, "ending_time": 1667575270339, "label": "3.6s \/ 131.3 MB"}, {"starting_time": 1667575270339, "ending_time": 1667575270672}]},
+        {"label": "fisher (9)", "cached": false, "index": 2, "times": [{"starting_time": 1667575270679, "ending_time": 1667575270772}, {"starting_time": 1667575270772, "ending_time": 1667575273827, "label": "3.5s \/ 136 MB"}, {"starting_time": 1667575273827, "ending_time": 1667575274172}]},
+        {"label": "fisher (6)", "cached": false, "index": 2, "times": [{"starting_time": 1667575274179, "ending_time": 1667575274272}, {"starting_time": 1667575274272, "ending_time": 1667575277313, "label": "3.5s \/ 136.2 MB"}, {"starting_time": 1667575277313, "ending_time": 1667575277681}]},
+        {"label": "fisher (8)", "cached": false, "index": 2, "times": [{"starting_time": 1667575277688, "ending_time": 1667575277781}, {"starting_time": 1667575277781, "ending_time": 1667575280774, "label": "3.4s \/ 135.8 MB"}, {"starting_time": 1667575280774, "ending_time": 1667575281131}]},
+        {"label": "fisher (13)", "cached": false, "index": 2, "times": [{"starting_time": 1667575281138, "ending_time": 1667575281232}, {"starting_time": 1667575281232, "ending_time": 1667575284315, "label": "3.5s \/ 135.5 MB"}, {"starting_time": 1667575284315, "ending_time": 1667575284662}]},
+        {"label": "fisher (14)", "cached": false, "index": 2, "times": [{"starting_time": 1667575284669, "ending_time": 1667575284762}, {"starting_time": 1667575284762, "ending_time": 1667575287816, "label": "3.5s \/ 139.5 MB"}, {"starting_time": 1667575287816, "ending_time": 1667575288181}]},
+        {"label": "fisher (1)", "cached": false, "index": 2, "times": [{"starting_time": 1667575288189, "ending_time": 1667575288281}, {"starting_time": 1667575288281, "ending_time": 1667575401609, "label": "1m 54s \/ 178.7 MB"}, {"starting_time": 1667575401609, "ending_time": 1667575401942}]},
+        {"label": "fisher (15)", "cached": false, "index": 2, "times": [{"starting_time": 1667575401951, "ending_time": 1667575402041}, {"starting_time": 1667575402041, "ending_time": 1667575405046, "label": "3.5s \/ 136.3 MB"}, {"starting_time": 1667575405046, "ending_time": 1667575405411}]},
+        {"label": "fisher (11)", "cached": false, "index": 2, "times": [{"starting_time": 1667575405419, "ending_time": 1667575405511}, {"starting_time": 1667575405511, "ending_time": 1667575408514, "label": "3.5s \/ 135.2 MB"}, {"starting_time": 1667575408514, "ending_time": 1667575408911}]},
+        {"label": "fisher (12)", "cached": false, "index": 2, "times": [{"starting_time": 1667575408920, "ending_time": 1667575409011}, {"starting_time": 1667575409011, "ending_time": 1667575412031, "label": "3.5s \/ 135.8 MB"}, {"starting_time": 1667575412031, "ending_time": 1667575412382}]},
+        {"label": "fisher (17)", "cached": false, "index": 2, "times": [{"starting_time": 1667575412390, "ending_time": 1667575412481}, {"starting_time": 1667575412481, "ending_time": 1667575415477, "label": "3.5s \/ 135.6 MB"}, {"starting_time": 1667575415477, "ending_time": 1667575415872}]},
+        {"label": "fisher (18)", "cached": false, "index": 2, "times": [{"starting_time": 1667575415891, "ending_time": 1667575415972}, {"starting_time": 1667575415972, "ending_time": 1667575419064, "label": "3.5s \/ 135.6 MB"}, {"starting_time": 1667575419064, "ending_time": 1667575419421}]},
+        {"label": "fisher (19)", "cached": false, "index": 2, "times": [{"starting_time": 1667575419429, "ending_time": 1667575419521}, {"starting_time": 1667575419521, "ending_time": 1667575422613, "label": "3.6s \/ 135.5 MB"}, {"starting_time": 1667575422613, "ending_time": 1667575423002}]},
+        {"label": "fisher (20)", "cached": false, "index": 2, "times": [{"starting_time": 1667575423009, "ending_time": 1667575423102}, {"starting_time": 1667575423102, "ending_time": 1667575426134, "label": "3.5s \/ 136.6 MB"}, {"starting_time": 1667575426134, "ending_time": 1667575426502}]},
+        {"label": "fisher (22)", "cached": false, "index": 2, "times": [{"starting_time": 1667575426509, "ending_time": 1667575426602}, {"starting_time": 1667575426602, "ending_time": 1667575429623, "label": "3.5s \/ 135.9 MB"}, {"starting_time": 1667575429623, "ending_time": 1667575429991}]},
+        {"label": "fisher (21)", "cached": false, "index": 2, "times": [{"starting_time": 1667575429999, "ending_time": 1667575430092}, {"starting_time": 1667575430092, "ending_time": 1667575433180, "label": "3.5s \/ 136.2 MB"}, {"starting_time": 1667575433180, "ending_time": 1667575433541}]},
+        {"label": "fisher (23)", "cached": false, "index": 2, "times": [{"starting_time": 1667575433548, "ending_time": 1667575433642}, {"starting_time": 1667575433642, "ending_time": 1667575436687, "label": "3.5s \/ 135.4 MB"}, {"starting_time": 1667575436687, "ending_time": 1667575437091}]},
+        {"label": "fisher (24)", "cached": false, "index": 2, "times": [{"starting_time": 1667575437097, "ending_time": 1667575437192}, {"starting_time": 1667575437192, "ending_time": 1667575440202, "label": "3.5s \/ 135.9 MB"}, {"starting_time": 1667575440202, "ending_time": 1667575440552}]},
+        {"label": "fisher (25)", "cached": false, "index": 2, "times": [{"starting_time": 1667575440559, "ending_time": 1667575440651}, {"starting_time": 1667575440651, "ending_time": 1667575443653, "label": "3.5s \/ 136 MB"}, {"starting_time": 1667575443653, "ending_time": 1667575444011}]},
+        {"label": "fisher (26)", "cached": false, "index": 2, "times": [{"starting_time": 1667575444018, "ending_time": 1667575444112}, {"starting_time": 1667575444112, "ending_time": 1667575447086, "label": "3.4s \/ 135.9 MB"}, {"starting_time": 1667575447086, "ending_time": 1667575447402}]},
+        {"label": "fisher (27)", "cached": false, "index": 2, "times": [{"starting_time": 1667575447408, "ending_time": 1667575447502}, {"starting_time": 1667575447502, "ending_time": 1667575450507, "label": "3.5s \/ 136.1 MB"}, {"starting_time": 1667575450507, "ending_time": 1667575450921}]},
+        {"label": "fisher (28)", "cached": false, "index": 2, "times": [{"starting_time": 1667575450928, "ending_time": 1667575451021}, {"starting_time": 1667575451021, "ending_time": 1667575453963, "label": "3.4s \/ 137.2 MB"}, {"starting_time": 1667575453963, "ending_time": 1667575454312}]},
+        {"label": "tsv_compress (1)", "cached": false, "index": 4, "times": [{"starting_time": 1667575455084, "ending_time": 1667575455113}, {"starting_time": 1667575455113, "ending_time": 1667575455466, "label": "797ms \/ 5 MB"}, {"starting_time": 1667575455466, "ending_time": 1667575455881}]},
+        {"label": "tsv2vcf (1)", "cached": false, "index": 5, "times": [{"starting_time": 1667575455888, "ending_time": 1667575455981}, {"starting_time": 1667575455981, "ending_time": 1667575458494, "label": "3s \/ 7.4 MB"}, {"starting_time": 1667575458494, "ending_time": 1667575458891}]},
+        {"label": "miami_plot (1)", "cached": false, "index": 6, "times": [{"starting_time": 1667575458897, "ending_time": 1667575458991}, {"starting_time": 1667575458991, "ending_time": 1667575463269, "label": "4.8s \/ 177.6 MB"}, {"starting_time": 1667575463269, "ending_time": 1667575463661}]}
     ]
 }
 ;
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/trace.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/trace.txt
index 21fbfdd9438e556c4fe50bd078d8d44c208e9f56..edf1e8b13eb1e0f4275f15aff5e3719065465013 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/trace.txt
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/trace.txt
@@ -1,35 +1,35 @@
 task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
-3	e4/8e01b2	21172	Backup	COMPLETED	0	2022-11-03 17:05:25.647	642ms	7ms	20.3%	0	0	152 KB	340 B
-1	e0/1dcdf1	21296	WorkflowVersion	COMPLETED	0	2022-11-03 17:05:26.300	957ms	423ms	19.1%	3.5 MB	13.5 MB	185.9 KB	1.5 KB
-2	ef/c033de	21504	vcf_subfield_title (1)	COMPLETED	0	2022-11-03 17:05:27.269	3.7s	3.3s	39.3%	103.8 MB	220.7 MB	12.1 MB	3.1 KB
-12	78/b090f4	21844	fisher (9)	COMPLETED	0	2022-11-03 17:05:31.138	3.9s	3.3s	143.9%	129.5 MB	1.3 GB	16.2 MB	648 B
-6	36/11f123	22135	fisher (3)	COMPLETED	0	2022-11-03 17:05:35.007	3.7s	3.2s	146.3%	130 MB	1.4 GB	16.2 MB	648 B
-13	c2/063e66	22429	fisher (10)	COMPLETED	0	2022-11-03 17:05:38.738	3.8s	3.3s	145.2%	127.2 MB	1.3 GB	16.2 MB	648 B
-5	72/11f420	22722	fisher (2)	COMPLETED	0	2022-11-03 17:05:42.496	3.7s	3.2s	148.3%	126.2 MB	1.4 GB	16.2 MB	648 B
-4	a1/6d1200	23017	fisher (1)	COMPLETED	0	2022-11-03 17:05:46.166	2m 1s	2m	57.8%	182.5 MB	1.4 GB	16.6 MB	13.1 MB
-16	9c/09efe4	24878	fisher (13)	COMPLETED	0	2022-11-03 17:07:46.866	3.6s	3.1s	149.9%	134.1 MB	1.4 GB	16.2 MB	648 B
-17	b5/d27919	25173	fisher (14)	COMPLETED	0	2022-11-03 17:07:50.436	3.5s	3.1s	152.4%	136.5 MB	1.4 GB	16.2 MB	648 B
-15	b5/b6744a	25466	fisher (12)	COMPLETED	0	2022-11-03 17:07:53.955	3.5s	3.1s	152.3%	136 MB	1.4 GB	16.2 MB	648 B
-14	78/e70240	25760	fisher (11)	COMPLETED	0	2022-11-03 17:07:57.506	3.7s	3.2s	148.1%	131.1 MB	1.4 GB	16.2 MB	648 B
-19	bc/4a42c4	26055	fisher (16)	COMPLETED	0	2022-11-03 17:08:01.176	3.5s	3.1s	153.7%	135.6 MB	1.4 GB	16.2 MB	648 B
-8	4e/ee34ed	26349	fisher (5)	COMPLETED	0	2022-11-03 17:08:04.706	3.6s	3.2s	148.2%	133.3 MB	1.4 GB	16.2 MB	648 B
-11	03/ea264b	26643	fisher (8)	COMPLETED	0	2022-11-03 17:08:08.341	3.5s	3.1s	146.2%	129.8 MB	1.4 GB	16.2 MB	648 B
-9	aa/28aed1	26937	fisher (6)	COMPLETED	0	2022-11-03 17:08:11.847	3.6s	3.2s	147.5%	133.5 MB	1.4 GB	16.2 MB	648 B
-10	58/6fbf6b	27229	fisher (7)	COMPLETED	0	2022-11-03 17:08:15.458	3.6s	3.1s	151.9%	133.4 MB	1.4 GB	16.2 MB	648 B
-7	b2/299532	27521	fisher (4)	COMPLETED	0	2022-11-03 17:08:19.037	3.6s	3.1s	147.5%	134.4 MB	1.4 GB	16.2 MB	648 B
-18	8a/a2977e	27815	fisher (15)	COMPLETED	0	2022-11-03 17:08:22.616	3.6s	3.2s	147.1%	135.6 MB	1.4 GB	16.2 MB	648 B
-20	2e/4ab4b3	28108	fisher (17)	COMPLETED	0	2022-11-03 17:08:26.266	3.5s	3.1s	152.0%	134.8 MB	1.4 GB	16.2 MB	648 B
-21	f7/e9d070	28401	fisher (18)	COMPLETED	0	2022-11-03 17:08:29.817	3.5s	3s	153.8%	135.7 MB	1.4 GB	16.2 MB	648 B
-22	c1/58c576	28694	fisher (19)	COMPLETED	0	2022-11-03 17:08:33.306	3.6s	3.1s	149.8%	132 MB	1.4 GB	16.2 MB	648 B
-23	99/77a82a	28987	fisher (20)	COMPLETED	0	2022-11-03 17:08:36.876	3.6s	3.1s	148.5%	134.6 MB	1.4 GB	16.2 MB	648 B
-24	51/ad7aa4	29278	fisher (21)	COMPLETED	0	2022-11-03 17:08:40.506	3.5s	3s	152.4%	136 MB	1.4 GB	16.2 MB	648 B
-25	e9/1569b2	29570	fisher (22)	COMPLETED	0	2022-11-03 17:08:44.016	3.5s	3.1s	154.0%	134.8 MB	1.4 GB	16.2 MB	648 B
-26	ad/121fd1	29863	fisher (23)	COMPLETED	0	2022-11-03 17:08:47.555	3.5s	3s	156.8%	138.8 MB	1.4 GB	16.2 MB	648 B
-27	c9/8f6265	30156	fisher (24)	COMPLETED	0	2022-11-03 17:08:51.055	3.6s	3.1s	149.9%	134.9 MB	1.4 GB	16.2 MB	648 B
-28	1d/564b3c	30449	fisher (25)	COMPLETED	0	2022-11-03 17:08:54.706	3.6s	3.1s	149.8%	132.9 MB	1.4 GB	16.2 MB	648 B
-29	a9/db74b8	30742	fisher (26)	COMPLETED	0	2022-11-03 17:08:58.286	3.7s	3.2s	147.4%	129.3 MB	1.4 GB	16.2 MB	648 B
-30	4e/44a80d	31036	fisher (27)	COMPLETED	0	2022-11-03 17:09:02.008	3.7s	3.3s	143.9%	130.9 MB	1.4 GB	16.2 MB	648 B
-31	52/e45ccb	31329	fisher (28)	COMPLETED	0	2022-11-03 17:09:05.756	3.7s	3.2s	147.2%	135 MB	1.4 GB	16.2 MB	648 B
-33	7c/11086c	31632	tsv_compress (1)	COMPLETED	0	2022-11-03 17:09:10.252	877ms	381ms	66.8%	5.1 MB	10 MB	13.2 MB	1.1 MB
-34	39/b87f10	31782	tsv2vcf (1)	COMPLETED	0	2022-11-03 17:09:11.135	3.4s	2.9s	34.0%	7.5 MB	17.9 MB	28.1 MB	14.6 MB
-32	82/a1750e	32047	miami_plot (1)	COMPLETED	0	2022-11-03 17:09:14.545	4.7s	4.3s	63.5%	182.1 MB	317.5 MB	27.3 MB	51.3 KB
+2	3b/d18102	11839	vcf_subfield_title (1)	CACHED	0	2022-11-04 16:20:31.579	3.5s	3s	40.4%	103.1 MB	219.9 MB	12.1 MB	3.1 KB
+5	17/0f9148	12124	fisher (2)	CACHED	0	2022-11-04 16:20:35.143	3.5s	3s	154.2%	136.6 MB	1.4 GB	16.2 MB	646 B
+19	28/827bd6	12413	fisher (13)	CACHED	0	2022-11-04 16:20:38.669	3.5s	3s	157.0%	136.8 MB	1.4 GB	16.2 MB	646 B
+1	99/439dda	13012	WorkflowVersion	COMPLETED	0	2022-11-04 16:20:51.403	1.1s	453ms	17.9%	3.6 MB	13.5 MB	185.9 KB	1.5 KB
+3	9a/5b654f	13233	Backup	COMPLETED	0	2022-11-04 16:20:52.485	536ms	6ms	20.0%	0	0	152 KB	338 B
+6	52/2c38de	13359	fisher (3)	COMPLETED	0	2022-11-04 16:20:53.030	3.5s	3s	155.5%	136 MB	1.4 GB	16.2 MB	646 B
+8	55/559994	13649	fisher (5)	COMPLETED	0	2022-11-04 16:20:56.510	3.5s	3s	153.6%	134.9 MB	1.4 GB	16.2 MB	646 B
+7	dc/c2eab9	13942	fisher (4)	COMPLETED	0	2022-11-04 16:20:59.980	3.5s	3s	155.7%	135.9 MB	1.4 GB	16.2 MB	646 B
+13	1e/fd5994	14234	fisher (10)	COMPLETED	0	2022-11-04 16:21:03.482	3.6s	3.1s	149.3%	133.1 MB	1.4 GB	16.2 MB	646 B
+10	7d/48d1cf	14527	fisher (7)	COMPLETED	0	2022-11-04 16:21:07.079	3.6s	3.2s	144.6%	131.3 MB	1.4 GB	16.2 MB	646 B
+12	94/ea5f77	14820	fisher (9)	COMPLETED	0	2022-11-04 16:21:10.679	3.5s	3.1s	153.9%	136 MB	1.4 GB	16.2 MB	646 B
+9	72/779535	15114	fisher (6)	COMPLETED	0	2022-11-04 16:21:14.179	3.5s	3s	155.1%	136.2 MB	1.4 GB	16.2 MB	646 B
+11	d9/7e2d0e	15409	fisher (8)	COMPLETED	0	2022-11-04 16:21:17.688	3.4s	3s	154.6%	135.8 MB	1.4 GB	16.2 MB	646 B
+17	06/09f270	15703	fisher (13)	COMPLETED	0	2022-11-04 16:21:21.138	3.5s	3.1s	149.8%	135.5 MB	1.4 GB	16.2 MB	646 B
+16	7b/1bf59a	15996	fisher (14)	COMPLETED	0	2022-11-04 16:21:24.669	3.5s	3.1s	151.1%	139.5 MB	1.4 GB	16.2 MB	646 B
+4	10/61ad6f	16289	fisher (1)	COMPLETED	0	2022-11-04 16:21:28.189	1m 54s	1m 53s	56.7%	178.7 MB	1.4 GB	16.6 MB	13.1 MB
+18	fa/658eee	18094	fisher (15)	COMPLETED	0	2022-11-04 16:23:21.951	3.5s	3s	153.1%	136.3 MB	1.4 GB	16.2 MB	646 B
+14	a8/0a235c	18388	fisher (11)	COMPLETED	0	2022-11-04 16:23:25.419	3.5s	3s	156.0%	135.2 MB	1.4 GB	16.2 MB	646 B
+15	ee/dd0f79	18682	fisher (12)	COMPLETED	0	2022-11-04 16:23:28.920	3.5s	3s	155.3%	135.8 MB	1.4 GB	16.2 MB	646 B
+20	73/b515a9	18975	fisher (17)	COMPLETED	0	2022-11-04 16:23:32.390	3.5s	3s	156.3%	135.6 MB	1.4 GB	16.2 MB	646 B
+21	05/3831aa	19268	fisher (18)	COMPLETED	0	2022-11-04 16:23:35.891	3.5s	3.1s	149.1%	135.6 MB	1.4 GB	16.2 MB	646 B
+22	94/c16c25	19561	fisher (19)	COMPLETED	0	2022-11-04 16:23:39.429	3.6s	3.1s	150.7%	135.5 MB	1.4 GB	16.2 MB	646 B
+23	2b/a27946	19855	fisher (20)	COMPLETED	0	2022-11-04 16:23:43.009	3.5s	3s	153.3%	136.6 MB	1.4 GB	16.2 MB	646 B
+25	29/3f925b	20148	fisher (22)	COMPLETED	0	2022-11-04 16:23:46.509	3.5s	3s	154.4%	135.9 MB	1.4 GB	16.2 MB	646 B
+24	85/8c0cf7	20440	fisher (21)	COMPLETED	0	2022-11-04 16:23:49.999	3.5s	3.1s	150.7%	136.2 MB	1.4 GB	16.2 MB	646 B
+26	91/bdc450	20733	fisher (23)	COMPLETED	0	2022-11-04 16:23:53.548	3.5s	3s	154.0%	135.4 MB	1.4 GB	16.2 MB	646 B
+27	e1/be1d29	21026	fisher (24)	COMPLETED	0	2022-11-04 16:23:57.097	3.5s	3s	152.8%	135.9 MB	1.4 GB	16.2 MB	646 B
+28	68/3f0978	21319	fisher (25)	COMPLETED	0	2022-11-04 16:24:00.559	3.5s	3s	155.1%	136 MB	1.4 GB	16.2 MB	646 B
+29	84/3dec27	21612	fisher (26)	COMPLETED	0	2022-11-04 16:24:04.018	3.4s	3s	156.8%	135.9 MB	1.4 GB	16.2 MB	646 B
+30	47/88cf99	21905	fisher (27)	COMPLETED	0	2022-11-04 16:24:07.408	3.5s	3s	155.2%	136.1 MB	1.4 GB	16.2 MB	646 B
+31	94/f91af0	22198	fisher (28)	COMPLETED	0	2022-11-04 16:24:10.928	3.4s	2.9s	157.8%	137.2 MB	1.4 GB	16.2 MB	646 B
+33	5c/3c2a26	22501	tsv_compress (1)	COMPLETED	0	2022-11-04 16:24:15.084	797ms	353ms	67.5%	5 MB	10 MB	13.2 MB	1.1 MB
+34	f0/b2c43f	22649	tsv2vcf (1)	COMPLETED	0	2022-11-04 16:24:15.888	3s	2.5s	31.7%	7.4 MB	17.9 MB	28.1 MB	14.6 MB
+32	9a/ba59a6	22913	miami_plot (1)	COMPLETED	0	2022-11-04 16:24:18.897	4.8s	4.3s	63.4%	177.6 MB	313.8 MB	27.3 MB	60.4 KB
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_subfield_title_report.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_subfield_title_report.txt
index d54f95275accf3ae573dacdb9754ed62416ab284..fb2482c348b2c85aa772da7d1239606e6dcb1c64 100644
--- a/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_subfield_title_report.txt
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_subfield_title_report.txt
@@ -12,7 +12,7 @@
 
 
 
-2022-11-03 16:05:30
+2022-11-04 15:20:34
 
 
 
@@ -31,7 +31,7 @@
 
 
 
-END TIME: 2022-11-03 16:05:30
+END TIME: 2022-11-04 15:20:34
 
 
 
@@ -106,7 +106,7 @@ loaded via a namespace (and not attached):
 
 ################################ JOB END
 
-TIME: 2022-11-03 16:05:30
+TIME: 2022-11-04 15:20:34
 
 TOTAL TIME LAPSE: 0S
 
diff --git a/fisher_for_vcf.config b/fisher_for_vcf.config
index d4520e818d361a67df9fe26ea0b241dbc1d5e5c9..532c297f654ad1e15a4f3d3ed538081fd5fca271 100644
--- a/fisher_for_vcf.config
+++ b/fisher_for_vcf.config
@@ -23,11 +23,13 @@ env {
     //chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" or /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt
     region = "none" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "none" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
     tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required. Warning: use a single space between string
-    x_lim = "chr7" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
+    x_lim = "whole" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
     bottom_y_column = "AF" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file. Then, explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
     color_column = "NULL" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
     y_lim1 = "NULL" // y-axis limits of the top panel in the miami plot, made of two numbers, separated by a single space. Example: y_lim1 = "0 3". Write "NULL" for no particular limit
     y_lim2 = "NULL" // y-axis limits of the bottom panel in the miami plot, made of two numbers, separated by a single space. Example: y_lim2 = "0 3" .Write "NULL" for no particular limit. Not considered if bottom_y_column = "NULL"
+    y_log1 = "FALSE" // either "TRUE" or "FALSE", y-axis log10 scale for the top panel in the miami plot. Example: y_log1 = "TRUE"
+    y_log2 = "TRUE" // either "TRUE" or "FALSE", y-axis log10 scale for the bottom panel in the miami plot. Example: y_log2 = "TRUE"
     cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 }
 
@@ -153,7 +155,7 @@ process {
         queue = "$queue"
         clusterOptions = "$qos $add_options"
         scratch=false
-        maxRetries=30
+        maxRetries=2
         errorStrategy='retry'
     }else{
         maxRetries=0
diff --git a/fisher_for_vcf.nf b/fisher_for_vcf.nf
index 7dc461873ac10b128739271a4dc625b395e5c341..3e5e3720229fcf48ff188594d18dfae5300d5bf3 100644
--- a/fisher_for_vcf.nf
+++ b/fisher_for_vcf.nf
@@ -124,6 +124,12 @@ if( ! y_lim1 in String ){
 if( ! y_lim2 in String ){
     error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim2 PARAMETER IN nextflow.config FILE:\n${y_lim2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
 }
+if( ! y_log1 in String ){
+    error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_log1 PARAMETER IN nextflow.config FILE:\n${y_log1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
+if( ! y_log2 in String ){
+    error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_log2 PARAMETER IN nextflow.config FILE:\n${y_log2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
+}
 def file_exists5 = cute.exists()
 if( ! file_exists5){
     error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID cute_path PARAMETER IN nextflow.config FILE:\n${cute_path}\nIF POINTING TO A DISTANT SERVER, CHECK THAT IT IS MOUNTED\n\n========\n\n"
@@ -249,6 +255,8 @@ process miami_plot {
     val color_column
     val y_lim1
     val y_lim2
+    val y_log1
+    val y_log2
     file cute
 
     output:
@@ -258,7 +266,7 @@ process miami_plot {
     script:
     """
     #!/bin/bash -ue
-    miami.R ${fisher} ${chr} "${x_lim_val}" "${bottom_y_column}" "${color_column}" "${y_lim1}" "${y_lim2}" "${cute}" "miami_report.txt"
+    miami.R ${fisher} ${chr} "${x_lim_val}" "${bottom_y_column}" "${color_column}" "${y_lim1}" "${y_lim2}" "${y_log1}" "${y_log2}" "${cute}" "miami_report.txt"
     """
 }