diff --git a/README.md b/README.md
index d156cdd449cb4a2327dd557c53fa3a70020c376e..17e3fc7cf1428d7bf7ee179b71bd6d93342ba019 100644
--- a/README.md
+++ b/README.md
@@ -145,7 +145,7 @@ export CONF_BEFORE=/opt/gensoft/exe # on maestro
 
 export JAVA_CONF=java/13.0.2
 export JAVA_CONF_AFTER=bin/java # on maestro
-export SINGU_CONF=singularity/3.8.3
+export SINGU_CONF=singularity
 export SINGU_CONF_AFTER=bin/singularity # on maestro
 export GIT_CONF=git/2.25.0
 export GIT_CONF_AFTER=bin/git # on maestro
@@ -161,10 +161,10 @@ Then run:
 
 ```bash
 # distant fisher_for_vcf.nf file
-/fisher_for_vcf/" ; nextflow run --modules ${MODULES} -hub pasteur gmillot/fisher_for_vcf -r v1.0 -c $HOME/fisher_for_vcf.config ; HOME="/pasteur/appa/homes/gmillot/"
+HOME="${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/" ; nextflow run --modules ${MODULES} fisher_for_vcf.nf -c fisher_for_vcf.config ; HOME="/pasteur/appa/homes/gmillot/"
+HOME="${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
 ```
 
 If an error message appears, like:
@@ -176,6 +176,30 @@ Purge using:
 rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot*
 ```
 
+
+### To get the miamiplot only
+
+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"
+x_lim="chr1"
+bottom_y_column="AF"
+color_column="NULL"
+y_lim1="NULL"
+y_lim2="NULL"
+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
+```
+
+The outputs files are in $PWD, i.e., where the code has been executed.
+
 <br /><br />
 ## OUTPUT
 
@@ -260,6 +284,12 @@ Gitlab developers
 ## WHAT'S NEW IN
 
 
+### v2.2
+
+bug fixed in miamiplot
+Now possible to get the miamiplot only (see the README file)
+
+
 ### v2.1
 
 Miamiplot improved for right display of the color legend
diff --git a/bin/miami.R b/bin/miami.R
index cf03453c414057d471ed879e41ceb3299f2b30a4..0bcb1f1853486e713c5c50c1f56685ba06760681 100644
--- a/bin/miami.R
+++ b/bin/miami.R
@@ -261,21 +261,15 @@ if(all(color.column != "NULL")){
 }else{
     color.column <- NULL
 }
-if(all(y.lim1 == "NULL")){
-    y.lim1 = NA
-}else if(length(y.lim1) != 1 & any(grepl(y.lim1, pattern = "\\D"))){# normally no NA with is.null()
-    tempo.cat <- paste0("ERROR IN miami.R:\nTHE y_lim1 PARAMETER MUST BE A SINGLE INTEGER\nHERE IT IS: \n", paste0(y.lim1, collapse = " "))
-    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(all(y.lim1 != "NULL")){
+    tempo <- fun_check(data = y.lim1, class = "vector", typeof = "character", length = 1) ; eval(ee)
 }else{
-    y.lim1 <- as.integer(y.lim1)
+    y.lim1 <- NULL
 }
-if(all(y.lim2 == "NULL")){
-    y.lim2 = NA
-}else if(length(y.lim2) != 1 & any(grepl(y.lim2, pattern = "\\D"))){# normally no NA with is.null()
-    tempo.cat <- paste0("ERROR IN miami.R:\nTHE y_lim2 PARAMETER MUST BE A SINGLE INTEGER\nHERE IT IS: \n", paste0(y.lim2, collapse = " "))
-    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(all(y.lim2 != "NULL")){
+    tempo <- fun_check(data = y.lim2, class = "vector", typeof = "character", length = 1) ; eval(ee)
 }else{
-    y.lim2 <- as.integer(y.lim2)
+    y.lim2 <- NULL
 }
 tempo <- fun_check(data = log, class = "vector", typeof = "character", length = 1) ; eval(ee)
 if(any(arg.check) == TRUE){ # normally no NA
@@ -289,8 +283,6 @@ if(any(arg.check) == TRUE){ # normally no NA
 tempo.arg <-c(
     "fisher",
     "chr.path", 
-    "y.lim1", 
-    "y.lim2",
     "log"
 )
 tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
@@ -359,7 +351,7 @@ if(erase.graphs == TRUE){
 
 
 if( ! file.exists(fisher)){
-    stop(paste0("\n\n============\n\nERROR IN miami.R\nFILE INDICATED IN THE cute PARAMETER DOES NOT EXISTS: ", fisher, "\n\n============\n\n"), call. = FALSE)
+    stop(paste0("\n\n============\n\nERROR IN miami.R\nFILE INDICATED IN THE fisher PARAMETER DOES NOT EXISTS: ", fisher, "\n\n============\n\n"), call. = FALSE)
 }else{
     obs <- read.table(fisher, sep = "\t", stringsAsFactors = FALSE, header = TRUE, comment.char = "")
     if(length(obs) > 0 & nrow(obs) > 0){
@@ -369,7 +361,7 @@ if( ! file.exists(fisher)){
     }
 }
 if( ! file.exists(chr.path)){
-    stop(paste0("\n\n============\n\nERROR IN miami.R\nFILE INDICATED IN THE cute PARAMETER DOES NOT EXISTS: ", chr.path, "\n\n============\n\n"), call. = FALSE)
+    stop(paste0("\n\n============\n\nERROR IN miami.R\nFILE INDICATED IN THE chr.path PARAMETER DOES NOT EXISTS: ", chr.path, "\n\n============\n\n"), call. = FALSE)
 }else{
     chr <- read.table(chr.path, sep = "\t", stringsAsFactors = FALSE, header = TRUE, comment.char = "")
 }
@@ -472,6 +464,29 @@ if(length(obs) > 0 & nrow(obs) > 0){
     }
 }
 
+if( ! is.null(y.lim1)){
+    print(y.lim1)
+    tempo <- unlist(strsplit(x = y.lim1, split = " "))
+    print(tempo)
+    if(length(tempo) != 2 | ! all(grepl(tempo, pattern = "^[0123456789.\\-\\+eE]*$"))){
+        tempo.cat <- paste0("ERROR IN miami.R:\nTHE y_lim1 PARAMETER MUST BE TWO NUMERIC VALUES SEPARATED BY A SINGLE SPACE\nHERE IT IS: \n", paste0(y.lim1, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        y.lim1 <- as.numeric(tempo)
+        print(y.lim1)
+    }
+}
+if( ! is.null(y.lim2)){
+    tempo <- unlist(strsplit(x = y.lim2, split = " "))
+    if(length(tempo) != 2 | ! all(grepl(tempo, pattern = "^[0123456789.\\-\\+eE]*$"))){
+        tempo.cat <- paste0("ERROR IN miami.R:\nTHE y_lim1 PARAMETER MUST BE TWO NUMERIC VALUES SEPARATED BY A SINGLE SPACE\nHERE IT IS: \n", paste0(y.lim2, collapse = " "))
+        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{
+        y.lim2 <- as.numeric(tempo)
+    }
+}
+
+
 ############ end modifications of imported tables
 
 
@@ -507,7 +522,7 @@ if(empty.obs == TRUE){
     ))
     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 = c(0, y.lim1), # NA indicate that limits must correspond to data limits but ylim() already used
+        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
     ))
@@ -553,7 +568,7 @@ if(empty.obs == TRUE){
         ))
         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 = c(y.lim2, 0), # NA indicate that limits must correspond to data limits but ylim() already used
+            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
         ))
diff --git a/example of results/PL_family_WGS_fisher_1665057598/miami.png b/example of results/PL_family_WGS_fisher_1665057598/miami.png
deleted file mode 100644
index ea9bfb78e97abd74226b608bb858bf5bd738f4de..0000000000000000000000000000000000000000
Binary files a/example of results/PL_family_WGS_fisher_1665057598/miami.png and /dev/null differ
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/trace.txt b/example of results/PL_family_WGS_fisher_1665057598/reports/trace.txt
deleted file mode 100644
index 2b99ea86eb86fb2edc8183502b67c9301512fef6..0000000000000000000000000000000000000000
--- a/example of results/PL_family_WGS_fisher_1665057598/reports/trace.txt	
+++ /dev/null
@@ -1,35 +0,0 @@
-task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
-2	b0/9796a8	29964	vcf_subfield_title (1)	CACHED	0	2022-10-06 13:54:21.159	3.6s	3.1s	40.3%	102.9 MB	219.8 MB	12.1 MB	3.1 KB
-13	fd/bd7066	30248	fisher (10)	CACHED	0	2022-10-06 13:54:24.806	3.7s	3.2s	148.8%	130.1 MB	1.4 GB	16.2 MB	646 B
-11	be/94545c	3978	fisher (8)	CACHED	0	2022-10-06 13:57:13.554	3.4s	3s	158.0%	136.8 MB	1.4 GB	16.2 MB	646 B
-7	9d/6772a6	32302	fisher (4)	CACHED	0	2022-10-06 13:54:50.045	3.6s	3.1s	153.5%	135.6 MB	1.4 GB	16.2 MB	646 B
-14	6d/f4d52c	2518	fisher (11)	CACHED	0	2022-10-06 13:56:56.124	3.5s	3.1s	156.5%	136.7 MB	1.4 GB	16.2 MB	646 B
-6	2d/715582	1931	fisher (3)	CACHED	0	2022-10-06 13:56:48.814	3.7s	3.2s	148.0%	130.9 MB	1.4 GB	16.2 MB	646 B
-10	13/b251b9	31716	fisher (7)	CACHED	0	2022-10-06 13:54:42.866	3.6s	3.1s	152.3%	132.3 MB	1.4 GB	16.2 MB	646 B
-8	30/ebe965	31127	fisher (5)	CACHED	0	2022-10-06 13:54:35.665	3.6s	3.1s	150.9%	127 MB	1.4 GB	16.2 MB	646 B
-16	fd/49def0	30540	fisher (13)	CACHED	0	2022-10-06 13:54:28.495	3.5s	3s	155.7%	136.1 MB	1.4 GB	16.2 MB	646 B
-18	70/a5494a	3393	fisher (14)	CACHED	0	2022-10-06 13:57:06.513	3.5s	3s	156.0%	135.9 MB	1.4 GB	16.2 MB	646 B
-15	7b/ecdb83	3101	fisher (12)	CACHED	0	2022-10-06 13:57:03.054	3.5s	2.9s	159.7%	137.9 MB	1.4 GB	16.2 MB	646 B
-12	72/f0756c	30834	fisher (9)	CACHED	0	2022-10-06 13:54:32.036	3.6s	3.1s	151.6%	135.4 MB	1.4 GB	16.2 MB	646 B
-9	e4/4362e3	32008	fisher (6)	CACHED	0	2022-10-06 13:54:46.472	3.6s	3.1s	152.9%	132.6 MB	1.4 GB	16.2 MB	646 B
-5	c1/2ac029	2225	fisher (2)	CACHED	0	2022-10-06 13:56:52.525	3.6s	3.1s	152.4%	134.9 MB	1.4 GB	16.2 MB	646 B
-4	e9/d7b2c1	32594	fisher (1)	CACHED	0	2022-10-06 13:54:53.664	1m 55s	1m 55s	57.2%	182.7 MB	1.4 GB	16.6 MB	13.1 MB
-19	a0/557151	3685	fisher (16)	CACHED	0	2022-10-06 13:57:10.014	3.5s	3.1s	154.7%	135.9 MB	1.4 GB	16.2 MB	646 B
-17	d1/db851d	31421	fisher (15)	CACHED	0	2022-10-06 13:54:39.274	3.6s	3.1s	150.7%	135.7 MB	1.4 GB	16.2 MB	646 B
-24	17/ddc8cc	5437	fisher (21)	CACHED	0	2022-10-06 13:57:31.254	3.6s	3.1s	149.5%	135.5 MB	1.4 GB	16.2 MB	646 B
-21	5d/c3e8fd	4561	fisher (18)	CACHED	0	2022-10-06 13:57:20.544	3.6s	3s	154.0%	135.7 MB	1.4 GB	16.2 MB	646 B
-31	ec/2468b4	7189	fisher (28)	CACHED	0	2022-10-06 13:57:52.754	3.5s	3.1s	151.7%	132.5 MB	1.4 GB	16.2 MB	646 B
-27	47/6d1521	6313	fisher (24)	CACHED	0	2022-10-06 13:57:42.074	3.6s	3.1s	147.7%	133.6 MB	1.4 GB	16.2 MB	646 B
-23	cb/ad799c	5145	fisher (20)	CACHED	0	2022-10-06 13:57:27.704	3.5s	3.1s	153.2%	136 MB	1.4 GB	16.2 MB	646 B
-22	71/31955f	4853	fisher (19)	CACHED	0	2022-10-06 13:57:24.154	3.5s	3.1s	154.5%	136.1 MB	1.4 GB	16.2 MB	646 B
-29	a9/ff87d3	2809	fisher (26)	CACHED	0	2022-10-06 13:56:59.674	3.4s	2.9s	162.9%	137.1 MB	1.4 GB	16.2 MB	646 B
-20	05/c8a725	4270	fisher (17)	CACHED	0	2022-10-06 13:57:16.993	3.5s	3.1s	151.2%	135.3 MB	1.4 GB	16.2 MB	646 B
-26	4b/01dc81	5729	fisher (22)	CACHED	0	2022-10-06 13:57:34.854	3.6s	3.1s	152.0%	133 MB	1.4 GB	16.2 MB	646 B
-28	15/a41382	6605	fisher (25)	CACHED	0	2022-10-06 13:57:45.734	3.5s	3s	157.3%	137 MB	1.4 GB	16.2 MB	646 B
-30	be/d20a87	6898	fisher (27)	CACHED	0	2022-10-06 13:57:49.263	3.5s	3s	155.9%	135.8 MB	1.4 GB	16.2 MB	646 B
-25	64/786fb5	6021	fisher (23)	CACHED	0	2022-10-06 13:57:38.424	3.6s	3.2s	146.4%	133.8 MB	1.4 GB	16.2 MB	646 B
-34	cc/b5fc76	7490	tsv_compress (1)	CACHED	0	2022-10-06 13:57:57.115	892ms	358ms	66.1%	4.9 MB	10 MB	13.2 MB	1.1 MB
-32	90/a76ff2	7636	tsv2vcf (1)	CACHED	0	2022-10-06 13:57:58.023	3.2s	2.8s	34.9%	7.5 MB	17.9 MB	28.1 MB	14.6 MB
-1	42/7dc85d	8383	WorkflowVersion	COMPLETED	0	2022-10-06 13:59:59.943	1.3s	462ms	17.8%	4.8 MB	13.5 MB	185.9 KB	1.5 KB
-3	c1/8c8dd3	8643	Backup	COMPLETED	0	2022-10-06 14:00:01.228	519ms	6ms	9.8%	0	0	152 KB	337 B
-33	6d/b6d4ce	8770	miami_plot (1)	COMPLETED	0	2022-10-06 14:00:02.101	4.9s	4.4s	62.7%	180.2 MB	317.1 MB	27.3 MB	133.3 KB
diff --git a/example of results/PL_family_WGS_fisher_1665057598/res_fisher.vcf.gz b/example of results/PL_family_WGS_fisher_1665057598/res_fisher.vcf.gz
deleted file mode 100644
index 5d199bbc6f819d20b3ab43d90f8fb3d509487924..0000000000000000000000000000000000000000
Binary files a/example of results/PL_family_WGS_fisher_1665057598/res_fisher.vcf.gz and /dev/null differ
diff --git a/example of results/PL_family_WGS_fisher_1665057598/res_fisher.vcf.gz.tbi b/example of results/PL_family_WGS_fisher_1665057598/res_fisher.vcf.gz.tbi
deleted file mode 100644
index 00abfa0cb0cf4392b748d338efa7d2162df21704..0000000000000000000000000000000000000000
Binary files a/example of results/PL_family_WGS_fisher_1665057598/res_fisher.vcf.gz.tbi and /dev/null differ
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/miami.png b/example_of_results/PL_family_WGS_fisher_1667491523/miami.png
new file mode 100644
index 0000000000000000000000000000000000000000..496f0296dc9a22592d99636ca57ba979af716e96
Binary files /dev/null and b/example_of_results/PL_family_WGS_fisher_1667491523/miami.png differ
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/Log_info.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/Log_info.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/Log_info.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/Log_info.txt
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/Run_info.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/Run_info.txt
similarity index 89%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/Run_info.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/Run_info.txt
index 0b06c4e3362134f1477cc5c554dca606e03df71c..6c232b9a586c6266818285f89ba2e0a8ba946655 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/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):  v1.10-dirty
-Cmd line: nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config -resume
+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
 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_1665057598
+result path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1667491523
 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_1665057598
+out_path: /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/results/PL_family_WGS_fisher_1667491523
 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_1665057598/reports/dag.dot b/example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/dag.dot
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot
index a1d3551b203e9c60efeb422bf28270e7596cf190..f93eac5e44cee38634adc990094dbb98aeae078d 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/reports/dag.dot	
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/dag.dot
@@ -3,10 +3,6 @@ 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"];
-p23 [label="tsv2vcf"];
-p1 -> p23 [label="vcf_ch3"];
-
 p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
 p5 [label="vcf_subfield_title"];
 p1 -> p5 [label="vcf_ch1"];
@@ -15,6 +11,10 @@ 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"];
+
 p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.from"];
 p6 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="combine"];
 p2 -> p6 [label="region_ch"];
@@ -60,20 +60,20 @@ p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
 p12 -> p13;
 
 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"];
+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"];
 
 p13 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="into"];
-p23 [label="tsv2vcf"];
-p13 -> p23 [label="fisher_ch4"];
+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"];
 
 p15 [shape=point,label="",fixedsize=true,width=0.1];
 p22 [label="miami_plot"];
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/fisher_for_vcf.config b/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config
similarity index 83%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/fisher_for_vcf.config
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config
index 7ed83f9fe9335ff3e8cd9643ace0745debc197b6..2b510a719d271b19252eff9305e9bd5dd7e86f36 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/reports/fisher_for_vcf.config	
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_for_vcf.config
@@ -16,18 +16,18 @@
 
 // variables exported to the main.nf environment. See https://www.nextflow.io/docs/latest/config.html#scope-env
 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" // vcf. Example: /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz. Warning, if zipped (.gz) must be together with a .tbi file
+    sample_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" // vcf. Example: "/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz". Warning, if zipped (.gz) must be together with a .tbi file. Another example: "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
     ped_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.pedigree.txt" // pedigree
-    //ped_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" // pedigree
+    //ped_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" or /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.pedigree.txt
     chr_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
-    //chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
+    //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 = "chr1" // 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 = "AF" // 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 = 3 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
-    y_lim2 = 2 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
+    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"
     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"
 }
 
@@ -51,7 +51,7 @@ result_folder_name = "PL_family_WGS_fisher"
 //// slurm variables
 // see https://confluence.pasteur.fr/pages/viewpage.action?pageId=69304504
 queue = 'common,dedicated' // -p option of slurm. Example: queue = 'common,dedicated'. Example: queue = 'hubbioit'
-qos = '--qos=ultrafast' // --qos option of slurm. Example: qos= '--qos=fast'. Example: qos = '--qos=ultrafast'. Example: qos = '--qos=hubbioit'
+qos = '--qos=ultrafast' // --qos option of slurm. Example: qos= '--qos=fast'. Example: qos = '--qos=ultrafast'. Example: qos = '--qos=hubbioit'. Warning, qos = '--qos=normal' only works with queue = 'common', not queue = 'common,dedicated'
 add_options = ' ' // additional option of slurm. Example: addoptions = '--exclude=maestro-1101,maestro-1034' or add_options = ' ', add_options = '--time=70:00:00' (acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds"). See https://slurm.schedmd.com/sbatch.html#OPT_time for other options
 //// end slurm variables
 
@@ -162,13 +162,13 @@ process {
     // all the processes of the main.nf file with the label 'bedtools' will use this directives by default
     withLabel: bash {
         container='gmillot/htslib_v1.0:gitlab_v9.1'
-        cpus=16 // only used when name = "local" in the executor part above
+        cpus=1 // only used when name = "local" in the executor part above
         memory='64G' // only used when name = "local" in the executor part above
     }
 
     withLabel: python {
         container='gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7'
-        cpus=16 // only used when name = "local" in the executor part above
+        cpus=1 // only used when name = "local" in the executor part above
         memory='64G' // only used when name = "local" in the executor part above
     }
 
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/fisher_report.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_report.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/fisher_report.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/fisher_report.txt
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/miami_report.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt
similarity index 82%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/miami_report.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt
index c14143595bd6ae769e272b4fbe338587d64223e4..0376b6b24e6cd2c75fe24770c4dd43c94184730e 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/reports/miami_report.txt	
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/miami_report.txt
@@ -12,7 +12,7 @@
 
 
 
-2022-10-06 12:00:04
+2022-11-03 16:09:17
 
 
 
@@ -31,7 +31,7 @@
 
 
 
-END TIME: 2022-10-06 12:00:06
+END TIME: 2022-11-03 16:09:18
 
 
 
@@ -64,15 +64,15 @@ 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,AF,AF,3,2,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,cute_little_R_functions.R,miami_report.txt 
 whole               chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr23, chr24, chr25, chrY, chrX, chrM 
 fisher              fisher.tsv 
 chr.path            hg19_grch37p5_chr_size_cumul.txt 
-x.lim               chr1 
+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 
 bottom.y.column     AF 
-color.column        AF 
-y.lim1              3 
-y.lim2              2 
+color.column        NULL 
+y.lim1              NULL 
+y.lim2              NULL 
 cute                cute_little_R_functions.R 
 log                 miami_report.txt
 
@@ -121,7 +121,7 @@ loaded via a namespace (and not attached):
 
 ################################ JOB END
 
-TIME: 2022-10-06 12:00:06
+TIME: 2022-11-03 16:09:18
 
 TOTAL TIME LAPSE: 2S
 
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/report.html b/example_of_results/PL_family_WGS_fisher_1667491523/reports/report.html
similarity index 97%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/report.html
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/report.html
index a3016ef1595ac327a4a3d5f4ad5b482b2c5819d8..2fda840127467d728aceda5f8da4b2daff598b0e 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/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 [peaceful_mahavira]">
+  <meta name="description" content="Nextflow workflow report for run id [clever_lamarck]">
   <meta name="author" content="Paolo Di Tommaso, Phil Ewels">
   <link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
 
-  <title>[peaceful_mahavira] Nextflow Workflow Report</title>
+  <title>[clever_lamarck] 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">
-        [peaceful_mahavira]
+        [clever_lamarck]
       </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>[peaceful_mahavira]</samp> <em>(resumed run)</em></h2>
+      <h2 class="text-muted mb-4"><samp>[clever_lamarck]</samp> </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">06-Oct-2022 13:59:58</span> - <span id="workflow_complete">06-Oct-2022 14:00:07</span>
-          (<span id="completed_fromnow"></span>duration: <strong>8.6s</strong>)
+          <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>)
         </dd>
 
         <dl>
           <div class="progress" style="height: 1.6rem; margin: 1.2rem auto; border-radius: 0.20rem;">
-            <div style="width: 8.82%" class="progress-bar bg-success" data-toggle="tooltip" data-placement="top" title="3 tasks succeeded"><span class="text-truncate">&nbsp; 3 succeeded &nbsp;</span></div>
-            <div style="width: 91.18%" class="progress-bar bg-secondary" data-toggle="tooltip" data-placement="top" title="31 tasks were cached"><span class="text-truncate">&nbsp; 31 cached &nbsp;</span></div>
+            <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: 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 -resume</code></pre></dd>
+        <dd><pre class="nfcommand"><code>nextflow run fisher_for_vcf.nf -c fisher_for_vcf.config</code></pre></dd>
       </dl>
 
       <dl class="row small">
         <dt class="col-sm-3">CPU-Hours</dt>
-        <dd class="col-sm-9"><samp>0.9 (99.6% cached)</samp></dd>
+        <dd class="col-sm-9"><samp>0.1</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>d57f38b4736ce9a3c384b0c56f200001</code></dd>
+          <dd class="col-sm-9"><code>54ec020277ef1fe7b6c5b3d8c11dfddc</code></dd>
         
 
         <dt class="col-sm-3">Workflow session</dt>
-        <dd class="col-sm-9"><code>84f1cdbf-4665-430f-804e-b9d0b03591c8</code></dd>
+        <dd class="col-sm-9"><code>c6d68cd5-4752-486f-bad7-d1ec5b02c7df</code></dd>
 
         
 
@@ -1029,7 +1029,7 @@ $(function() {
 
   // Nextflow report data
   window.data = { "trace":[
-{"task_id":"1","hash":"42\/7dc85d","native_id":"8383","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":"1665057599943","start":"1665057600054","complete":"1665057601218","duration":"1275","realtime":"462","%cpu":"17.8","%mem":"0.0","rss":"5025792","vmem":"14155776","peak_rss":"5025792","peak_vmem":"14168064","rchar":"190318","wchar":"1519","syscr":"367","syscw":"35","read_bytes":"4304896","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/42\/7dc85dfc1f0e85108d894b159fdf4d","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_1665057598\" >> 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_1665057598\\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":"16","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=chr1\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\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_1665057598\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":"b0\/9796a8","native_id":"29964","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":"1665057261159","start":"1665057261247","complete":"1665057264717","duration":"3558","realtime":"3079","%cpu":"40.3","%mem":"0.1","rss":"107945984","vmem":"230440960","peak_rss":"107945984","peak_vmem":"230473728","rchar":"12700711","wchar":"3190","syscr":"1666","syscw":"243","read_bytes":"16828416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/b0\/9796a80210d259d24c77c5d53d7f09","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"10178","inv_ctxt":"7"},{"task_id":"11","hash":"be\/94545c","native_id":"3978","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":"CACHED","exit":"0","submit":"1665057433554","start":"1665057433648","complete":"1665057436977","duration":"3423","realtime":"3002","%cpu":"158.0","%mem":"0.1","rss":"143425536","vmem":"1461825536","peak_rss":"143425536","peak_vmem":"1461858304","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52927488","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/be\/94545c0ccabbb2933f1cba151fdcff","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"13","hash":"fd\/bd7066","native_id":"30248","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":"CACHED","exit":"0","submit":"1665057264806","start":"1665057264816","complete":"1665057268478","duration":"3672","realtime":"3169","%cpu":"148.8","%mem":"0.1","rss":"136392704","vmem":"1455468544","peak_rss":"136392704","peak_vmem":"1455501312","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52617216","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/fd\/bd70663703943487b3d302ba7e5a54","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3149","inv_ctxt":"5"},{"task_id":"7","hash":"9d\/6772a6","native_id":"32302","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":"CACHED","exit":"0","submit":"1665057290045","start":"1665057290128","complete":"1665057293657","duration":"3612","realtime":"3092","%cpu":"153.5","%mem":"0.1","rss":"142225408","vmem":"1460789248","peak_rss":"142225408","peak_vmem":"1460822016","rchar":"16989826","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52717568","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/9d\/6772a636bf33087527f62f907e0caa","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3335","inv_ctxt":"18"},{"task_id":"6","hash":"2d\/715582","native_id":"1931","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":"CACHED","exit":"0","submit":"1665057408814","start":"1665057408897","complete":"1665057412518","duration":"3704","realtime":"3194","%cpu":"148.0","%mem":"0.1","rss":"137261056","vmem":"1454231552","peak_rss":"137261056","peak_vmem":"1454264320","rchar":"16989824","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52732928","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/2d\/715582b2a7d281920bb47513b01bab","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3119","inv_ctxt":"4"},{"task_id":"14","hash":"6d\/f4d52c","native_id":"2518","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":"CACHED","exit":"0","submit":"1665057416124","start":"1665057416207","complete":"1665057419667","duration":"3543","realtime":"3051","%cpu":"156.5","%mem":"0.1","rss":"143388672","vmem":"1461825536","peak_rss":"143388672","peak_vmem":"1461858304","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"53213184","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/6d\/f4d52cc4750cf040b6a0c01afd83b1","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3388","inv_ctxt":"3"},{"task_id":"10","hash":"13\/b251b9","native_id":"31716","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":"CACHED","exit":"0","submit":"1665057282866","start":"1665057282958","complete":"1665057286465","duration":"3599","realtime":"3114","%cpu":"152.3","%mem":"0.1","rss":"138706944","vmem":"1455468544","peak_rss":"138706944","peak_vmem":"1455501312","rchar":"16989826","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52642816","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/13\/b251b96a8f5f4955ebf86aa8262538","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3152","inv_ctxt":"4"},{"task_id":"16","hash":"fd\/49def0","native_id":"30540","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":"1665057268495","start":"1665057268578","complete":"1665057272027","duration":"3532","realtime":"3033","%cpu":"155.7","%mem":"0.1","rss":"142725120","vmem":"1461563392","peak_rss":"142725120","peak_vmem":"1461596160","rchar":"16989826","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"53009408","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/fd\/49def07dcd2ad4b7f9d24a31b6d221","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"4"},{"task_id":"8","hash":"30\/ebe965","native_id":"31127","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":"CACHED","exit":"0","submit":"1665057275665","start":"1665057275757","complete":"1665057279267","duration":"3602","realtime":"3122","%cpu":"150.9","%mem":"0.1","rss":"133214208","vmem":"1456136192","peak_rss":"133214208","peak_vmem":"1456168960","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52919296","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/30\/ebe965686a371d5dee34ee75259f47","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3236","inv_ctxt":"6"},{"task_id":"18","hash":"70\/a5494a","native_id":"3393","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":"CACHED","exit":"0","submit":"1665057426513","start":"1665057426607","complete":"1665057429997","duration":"3484","realtime":"3034","%cpu":"156.0","%mem":"0.1","rss":"142540800","vmem":"1461051392","peak_rss":"142540800","peak_vmem":"1461084160","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52698112","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/70\/a5494a653dac1a3ef72b5712afee7a","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3359","inv_ctxt":"5"},{"task_id":"15","hash":"7b\/ecdb83","native_id":"3101","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":"CACHED","exit":"0","submit":"1665057423054","start":"1665057423147","complete":"1665057426507","duration":"3453","realtime":"2948","%cpu":"159.7","%mem":"0.1","rss":"144601088","vmem":"1464365056","peak_rss":"144601088","peak_vmem":"1464397824","rchar":"16989826","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52797440","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/7b\/ecdb831c2ce27661d5ed19f9c78b1d","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3460","inv_ctxt":"0"},{"task_id":"12","hash":"72\/f0756c","native_id":"30834","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":"CACHED","exit":"0","submit":"1665057272036","start":"1665057272126","complete":"1665057275657","duration":"3621","realtime":"3118","%cpu":"151.6","%mem":"0.1","rss":"142028800","vmem":"1460789248","peak_rss":"142028800","peak_vmem":"1460822016","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52433920","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/72\/f0756c208af3e49580385d8cd5ea7c","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"4"},{"task_id":"9","hash":"e4\/4362e3","native_id":"32008","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":"CACHED","exit":"0","submit":"1665057286472","start":"1665057286565","complete":"1665057290028","duration":"3556","realtime":"3124","%cpu":"152.9","%mem":"0.1","rss":"139005952","vmem":"1455800320","peak_rss":"139005952","peak_vmem":"1455833088","rchar":"16989827","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52573184","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e4\/4362e3bccb213bdb6fbd81ec52be84","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3158","inv_ctxt":"9"},{"task_id":"5","hash":"c1\/2ac029","native_id":"2225","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":"1665057412525","start":"1665057412618","complete":"1665057416107","duration":"3582","realtime":"3108","%cpu":"152.4","%mem":"0.1","rss":"141492224","vmem":"1455800320","peak_rss":"141492224","peak_vmem":"1455833088","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52363264","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c1\/2ac0291a86b5283dd79e4a163588eb","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3223","inv_ctxt":"5"},{"task_id":"4","hash":"e9\/d7b2c1","native_id":"32594","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":"CACHED","exit":"0","submit":"1665057293664","start":"1665057293756","complete":"1665057408797","duration":"115133","realtime":"114676","%cpu":"57.2","%mem":"0.2","rss":"188751872","vmem":"1511907328","peak_rss":"191569920","peak_vmem":"1514819584","rchar":"17390817","wchar":"13700503","syscr":"2069","syscw":"1951","read_bytes":"52709376","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/e9\/d7b2c1f8f9241caa78794c8157015a","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"603732","inv_ctxt":"1612"},{"task_id":"19","hash":"a0\/557151","native_id":"3685","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":"CACHED","exit":"0","submit":"1665057430014","start":"1665057430097","complete":"1665057433548","duration":"3534","realtime":"3055","%cpu":"154.7","%mem":"0.1","rss":"142462976","vmem":"1461051392","peak_rss":"142462976","peak_vmem":"1461084160","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52448256","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/a0\/557151d2cc0dcf2a951e1f9ae7ce05","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3350","inv_ctxt":"5"},{"task_id":"17","hash":"d1\/db851d","native_id":"31421","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":"CACHED","exit":"0","submit":"1665057279274","start":"1665057279367","complete":"1665057282858","duration":"3584","realtime":"3142","%cpu":"150.7","%mem":"0.1","rss":"142290944","vmem":"1457176576","peak_rss":"142290944","peak_vmem":"1457209344","rchar":"16989827","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52681728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/d1\/db851d0d8138c9afe765204f287349","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3243","inv_ctxt":"1"},{"task_id":"24","hash":"17\/ddc8cc","native_id":"5437","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":"CACHED","exit":"0","submit":"1665057451254","start":"1665057451338","complete":"1665057454847","duration":"3593","realtime":"3124","%cpu":"149.5","%mem":"0.1","rss":"142049280","vmem":"1460527104","peak_rss":"142049280","peak_vmem":"1460559872","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52930560","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/17\/ddc8ccd0ab25cc5b5979e1875727e6","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3330","inv_ctxt":"5"},{"task_id":"21","hash":"5d\/c3e8fd","native_id":"4561","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":"CACHED","exit":"0","submit":"1665057440544","start":"1665057440628","complete":"1665057444147","duration":"3603","realtime":"3049","%cpu":"154.0","%mem":"0.1","rss":"142278656","vmem":"1461051392","peak_rss":"142278656","peak_vmem":"1461084160","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52501504","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/5d\/c3e8fd1d0ca2f833d5ee2a24605c41","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3"},{"task_id":"31","hash":"ec\/2468b4","native_id":"7189","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":"CACHED","exit":"0","submit":"1665057472754","start":"1665057472847","complete":"1665057476278","duration":"3524","realtime":"3051","%cpu":"151.7","%mem":"0.1","rss":"138973184","vmem":"1459609600","peak_rss":"138973184","peak_vmem":"1459642368","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52110336","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/ec\/2468b42a0bbbc293549bf98065e451","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3243","inv_ctxt":"6"},{"task_id":"23","hash":"cb\/ad799c","native_id":"5145","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":"CACHED","exit":"0","submit":"1665057447704","start":"1665057447787","complete":"1665057451238","duration":"3534","realtime":"3072","%cpu":"153.2","%mem":"0.1","rss":"142610432","vmem":"1461563392","peak_rss":"142610432","peak_vmem":"1461596160","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52943872","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/cb\/ad799c50a18d9dccb36e75666428aa","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3380","inv_ctxt":"1"},{"task_id":"27","hash":"47\/6d1521","native_id":"6313","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":"CACHED","exit":"0","submit":"1665057462074","start":"1665057462169","complete":"1665057465718","duration":"3644","realtime":"3140","%cpu":"147.7","%mem":"0.1","rss":"140111872","vmem":"1457176576","peak_rss":"140111872","peak_vmem":"1457209344","rchar":"16989826","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"53014528","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/47\/6d1521f37e0f1aaf9177b4c2cb40cf","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3248","inv_ctxt":"22"},{"task_id":"29","hash":"a9\/ff87d3","native_id":"2809","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":"CACHED","exit":"0","submit":"1665057419674","start":"1665057419767","complete":"1665057423048","duration":"3374","realtime":"2905","%cpu":"162.9","%mem":"0.1","rss":"143806464","vmem":"1463578624","peak_rss":"143806464","peak_vmem":"1463611392","rchar":"16989824","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52276224","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/a9\/ff87d3dbc303cd652fe88ce8134b82","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3389","inv_ctxt":"3"},{"task_id":"20","hash":"05\/c8a725","native_id":"4270","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":"CACHED","exit":"0","submit":"1665057436993","start":"1665057437077","complete":"1665057440528","duration":"3535","realtime":"3123","%cpu":"151.2","%mem":"0.1","rss":"141836288","vmem":"1460527104","peak_rss":"141836288","peak_vmem":"1460559872","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52966400","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/05\/c8a725b1f4cba377274afba36ec9f5","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3316","inv_ctxt":"5"},{"task_id":"22","hash":"71\/31955f","native_id":"4853","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":"CACHED","exit":"0","submit":"1665057444154","start":"1665057444247","complete":"1665057447688","duration":"3534","realtime":"3056","%cpu":"154.5","%mem":"0.1","rss":"142725120","vmem":"1461051392","peak_rss":"142725120","peak_vmem":"1461084160","rchar":"16989826","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52580352","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/71\/31955fa2bdb06f17f0b88fc6189580","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"4"},{"task_id":"26","hash":"4b\/01dc81","native_id":"5729","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":"CACHED","exit":"0","submit":"1665057454854","start":"1665057454947","complete":"1665057458408","duration":"3554","realtime":"3108","%cpu":"152.0","%mem":"0.1","rss":"139411456","vmem":"1456136192","peak_rss":"139411456","peak_vmem":"1456168960","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52681728","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/4b\/01dc81a6d4bbe09f82779a6309f6b0","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3225","inv_ctxt":"12"},{"task_id":"28","hash":"15\/a41382","native_id":"6605","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":"CACHED","exit":"0","submit":"1665057465734","start":"1665057465818","complete":"1665057469247","duration":"3513","realtime":"3031","%cpu":"157.3","%mem":"0.1","rss":"143691776","vmem":"1462190080","peak_rss":"143691776","peak_vmem":"1462222848","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"53113856","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/15\/a4138235b0e481e4b7beeb3a9f2e56","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3396","inv_ctxt":"3"},{"task_id":"30","hash":"be\/d20a87","native_id":"6898","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":"CACHED","exit":"0","submit":"1665057469263","start":"1665057469347","complete":"1665057472747","duration":"3484","realtime":"3045","%cpu":"155.9","%mem":"0.1","rss":"142344192","vmem":"1460789248","peak_rss":"142344192","peak_vmem":"1460822016","rchar":"16989824","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"52432896","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/be\/d20a87d8098418f30b8858b57c1b2a","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\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":"3326","inv_ctxt":"13"},{"task_id":"25","hash":"64\/786fb5","native_id":"6021","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":"CACHED","exit":"0","submit":"1665057458424","start":"1665057458509","complete":"1665057462068","duration":"3644","realtime":"3217","%cpu":"146.4","%mem":"0.1","rss":"140320768","vmem":"1458900992","peak_rss":"140320768","peak_vmem":"1458933760","rchar":"16989825","wchar":"646","syscr":"2013","syscw":"14","read_bytes":"53852160","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/64\/786fb57624eb37d149d7d2272a8030","script":"\n    #!\/bin\/bash -ue\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    ","scratch":"-","queue":"-","cpus":"16","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=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\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_1665057257\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"3298","inv_ctxt":"24"},{"task_id":"34","hash":"cc\/b5fc76","native_id":"7490","process":"tsv_compress","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv_compress (1)","status":"CACHED","exit":"0","submit":"1665057477115","start":"1665057477178","complete":"1665057478007","duration":"892","realtime":"358","%cpu":"66.1","%mem":"0.0","rss":"5181440","vmem":"10412032","peak_rss":"5181440","peak_vmem":"10436608","rchar":"13859961","wchar":"1196541","syscr":"683","syscw":"17","read_bytes":"580608","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/cc\/b5fc76509adda5178af8cc9bad1f42","script":"\n    #!\/bin\/bash -ue\n    gzip -cf9 fisher.tsv > res_fisher.tsv.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n    ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1665057257\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"108","inv_ctxt":"2"},{"task_id":"32","hash":"90\/a76ff2","native_id":"7636","process":"tsv2vcf","module":"-","container":"\/mnt\/c\/Users\/gmillot\/singularity\/gmillot-htslib_v1.0-gitlab_v9.1.img","tag":"-","name":"tsv2vcf (1)","status":"CACHED","exit":"0","submit":"1665057478023","start":"1665057478107","complete":"1665057481266","duration":"3243","realtime":"2769","%cpu":"34.9","%mem":"0.0","rss":"7856128","vmem":"18702336","peak_rss":"7856128","peak_vmem":"18735104","rchar":"29503424","wchar":"15355180","syscr":"2676","syscw":"18454","read_bytes":"1340416","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/90\/a76ff2c5c3a2e522bc7a4b4881777b","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=<FISHER=\" ;\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 $i ; if(i < NF){print \"|\"}} ;\n            print \"\\n\"\n        }\n    \' fisher.tsv >> res_fisher.vcf\n    bgzip -f -l 9 res_fisher.vcf > res_fisher.vcf.gz # htslib command, -l 9 best compression, -c to standard output, -f to force without asking\n    tabix -p vcf res_fisher.vcf.gz # htslib command\n    ","scratch":"-","queue":"-","cpus":"16","memory":"68719476736","disk":"-","time":"-","env":"sample_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz\nped_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/Dyslexia.pedigree.txt\nchr_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/dataset\/hg19_grch37p5_chr_size_cumul.txt\nregion=none\ntsv_extra_fields=AC AF CSQ_SIFT CSQ_PolyPhen\nx_lim=chr1\nbottom_y_column=AC\ncolor_column=NULL\ny_lim1=3\ny_lim2=2\ncute_path=https:\/\/gitlab.pasteur.fr\/gmillot\/cute_little_R_functions\/-\/raw\/v11.4.0\/cute_little_R_functions.R\nsystem_exec=local\nout_path_ini=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\nout_path=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/results\/PL_family_WGS_fisher_1665057257\nqueue=common,dedicated\nqos=--qos=ultrafast\nadd_options= \nPATH=\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/bin:$PATH\n","error_action":"-","vol_ctxt":"18617","inv_ctxt":"8"},{"task_id":"3","hash":"c1\/8c8dd3","native_id":"8643","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":"1665057601228","start":"1665057601319","complete":"1665057601747","duration":"519","realtime":"6","%cpu":"9.8","%mem":"0.0","rss":"0","vmem":"0","peak_rss":"0","peak_vmem":"0","rchar":"155652","wchar":"337","syscr":"252","syscw":"14","read_bytes":"521216","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/c1\/8c8dd313bbdd202c225f8eb4051305","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":"16","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=chr1\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\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_1665057598\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":"33","hash":"6d\/b6d4ce","native_id":"8770","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":"1665057602101","start":"1665057602147","complete":"1665057606998","duration":"4897","realtime":"4384","%cpu":"62.7","%mem":"0.2","rss":"185012224","vmem":"330903552","peak_rss":"188915712","peak_vmem":"332554240","rchar":"28603885","wchar":"136539","syscr":"5938","syscw":"239","read_bytes":"42125312","write_bytes":"0","attempt":"1","workdir":"\/mnt\/c\/Users\/Gael\/Documents\/Git_projects\/fisher_for_vcf\/work\/6d\/b6d4cef231ba35b8ea4c16e067f716","script":"\n    #!\/bin\/bash -ue\n    miami.R fisher.tsv hg19_grch37p5_chr_size_cumul.txt \"chr1\" \"AF\" \"AF\" \"3\" \"2\" \"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=chr1\nbottom_y_column=AF\ncolor_column=AF\ny_lim1=3\ny_lim2=2\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_1665057598\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":"6446","inv_ctxt":"11"}], "summary":[{"cpuUsage":{"mean":40.3,"min":40.3,"q1":40.3,"q2":40.3,"q3":40.3,"max":40.3,"minLabel":"vcf_subfield_title (1)","maxLabel":"vcf_subfield_title (1)","q1Label":"vcf_subfield_title (1)","q2Label":"vcf_subfield_title (1)","q3Label":"vcf_subfield_title 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+{"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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diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/timeline.html b/example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html
similarity index 96%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/timeline.html
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html
index b57af78f53f2c1694db817c2225611ecf47c5510..12188039a20a5f076a6f5b8f201be19ab31f7491 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/reports/timeline.html	
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/timeline.html
@@ -205,44 +205,44 @@ $(function() {
 
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+        {"label": "fisher (4)", "cached": false, "index": 3, "times": [{"starting_time": 1667491699037, "ending_time": 1667491699129}, {"starting_time": 1667491699129, "ending_time": 1667491702213, "label": "3.6s \/ 134.4 MB"}, {"starting_time": 1667491702213, "ending_time": 1667491702609}]},
+        {"label": "fisher (15)", "cached": false, "index": 3, "times": [{"starting_time": 1667491702616, "ending_time": 1667491702710}, {"starting_time": 1667491702710, "ending_time": 1667491705910, "label": "3.6s \/ 135.6 MB"}, {"starting_time": 1667491705910, "ending_time": 1667491706259}]},
+        {"label": "fisher (17)", "cached": false, "index": 3, "times": [{"starting_time": 1667491706266, "ending_time": 1667491706359}, {"starting_time": 1667491706359, "ending_time": 1667491709438, "label": "3.5s \/ 134.8 MB"}, {"starting_time": 1667491709438, "ending_time": 1667491709809}]},
+        {"label": "fisher (18)", "cached": false, "index": 3, "times": [{"starting_time": 1667491709817, "ending_time": 1667491709909}, {"starting_time": 1667491709909, "ending_time": 1667491712943, "label": "3.5s \/ 135.7 MB"}, {"starting_time": 1667491712943, "ending_time": 1667491713299}]},
+        {"label": "fisher (19)", "cached": false, "index": 3, "times": [{"starting_time": 1667491713306, "ending_time": 1667491713400}, {"starting_time": 1667491713400, "ending_time": 1667491716541, "label": "3.6s \/ 132 MB"}, {"starting_time": 1667491716541, "ending_time": 1667491716868}]},
+        {"label": "fisher (20)", "cached": false, "index": 3, "times": [{"starting_time": 1667491716876, "ending_time": 1667491716968}, {"starting_time": 1667491716968, "ending_time": 1667491720080, "label": "3.6s \/ 134.6 MB"}, {"starting_time": 1667491720080, "ending_time": 1667491720499}]},
+        {"label": "fisher (21)", "cached": false, "index": 3, "times": [{"starting_time": 1667491720506, "ending_time": 1667491720599}, {"starting_time": 1667491720599, "ending_time": 1667491723637, "label": "3.5s \/ 136 MB"}, {"starting_time": 1667491723637, "ending_time": 1667491724009}]},
+        {"label": "fisher (22)", "cached": false, "index": 3, "times": [{"starting_time": 1667491724016, "ending_time": 1667491724109}, {"starting_time": 1667491724109, "ending_time": 1667491727186, "label": "3.5s \/ 134.8 MB"}, {"starting_time": 1667491727186, "ending_time": 1667491727549}]},
+        {"label": "fisher (23)", "cached": false, "index": 3, "times": [{"starting_time": 1667491727555, "ending_time": 1667491727649}, {"starting_time": 1667491727649, "ending_time": 1667491730657, "label": "3.5s \/ 138.8 MB"}, {"starting_time": 1667491730657, "ending_time": 1667491731049}]},
+        {"label": "fisher (24)", "cached": false, "index": 3, "times": [{"starting_time": 1667491731055, "ending_time": 1667491731149}, {"starting_time": 1667491731149, "ending_time": 1667491734270, "label": "3.6s \/ 134.9 MB"}, {"starting_time": 1667491734270, "ending_time": 1667491734699}]},
+        {"label": "fisher (25)", "cached": false, "index": 3, "times": [{"starting_time": 1667491734706, "ending_time": 1667491734799}, {"starting_time": 1667491734799, "ending_time": 1667491737892, "label": "3.6s \/ 132.9 MB"}, {"starting_time": 1667491737892, "ending_time": 1667491738279}]},
+        {"label": "fisher (26)", "cached": false, "index": 3, "times": [{"starting_time": 1667491738286, "ending_time": 1667491738379}, {"starting_time": 1667491738379, "ending_time": 1667491741617, "label": "3.7s \/ 129.3 MB"}, {"starting_time": 1667491741617, "ending_time": 1667491742000}]},
+        {"label": "fisher (27)", "cached": false, "index": 3, "times": [{"starting_time": 1667491742008, "ending_time": 1667491742100}, {"starting_time": 1667491742100, "ending_time": 1667491745378, "label": "3.7s \/ 130.9 MB"}, {"starting_time": 1667491745378, "ending_time": 1667491745749}]},
+        {"label": "fisher (28)", "cached": false, "index": 3, "times": [{"starting_time": 1667491745756, "ending_time": 1667491745849}, {"starting_time": 1667491745849, "ending_time": 1667491749039, "label": "3.7s \/ 135 MB"}, {"starting_time": 1667491749039, "ending_time": 1667491749439}]},
+        {"label": "tsv_compress (1)", "cached": false, "index": 4, "times": [{"starting_time": 1667491750252, "ending_time": 1667491750340}, {"starting_time": 1667491750340, "ending_time": 1667491750721, "label": "877ms \/ 5.1 MB"}, {"starting_time": 1667491750721, "ending_time": 1667491751129}]},
+        {"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}]}
     ]
 }
 ;
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
new file mode 100644
index 0000000000000000000000000000000000000000..21fbfdd9438e556c4fe50bd078d8d44c208e9f56
--- /dev/null
+++ b/example_of_results/PL_family_WGS_fisher_1667491523/reports/trace.txt
@@ -0,0 +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
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/vcf_csq_subfield_titles.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_csq_subfield_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/vcf_csq_subfield_titles.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_csq_subfield_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/vcf_info_field_titles.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_info_field_titles.txt
similarity index 100%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/vcf_info_field_titles.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_info_field_titles.txt
diff --git a/example of results/PL_family_WGS_fisher_1665057598/reports/vcf_subfield_title_report.txt b/example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_subfield_title_report.txt
similarity index 96%
rename from example of results/PL_family_WGS_fisher_1665057598/reports/vcf_subfield_title_report.txt
rename to example_of_results/PL_family_WGS_fisher_1667491523/reports/vcf_subfield_title_report.txt
index d8a444221364f7cbfc6352b3404c9cf19fc1f825..d54f95275accf3ae573dacdb9754ed62416ab284 100644
--- a/example of results/PL_family_WGS_fisher_1665057598/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 @@
 
 
 
-2022-10-06 11:54:24
+2022-11-03 16:05:30
 
 
 
@@ -31,7 +31,7 @@
 
 
 
-END TIME: 2022-10-06 11:54:24
+END TIME: 2022-11-03 16:05:30
 
 
 
@@ -106,7 +106,7 @@ loaded via a namespace (and not attached):
 
 ################################ JOB END
 
-TIME: 2022-10-06 11:54:24
+TIME: 2022-11-03 16:05:30
 
 TOTAL TIME LAPSE: 0S
 
diff --git a/example of results/PL_family_WGS_fisher_1665057598/res_fisher.tsv.gz b/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.tsv.gz
similarity index 99%
rename from example of results/PL_family_WGS_fisher_1665057598/res_fisher.tsv.gz
rename to example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.tsv.gz
index 6a8ddbaec69dd61ecd64e6aaee7ffedc0288baf6..0efcce6a9f40fe4a4d2882a8d92c7ca8e4e31ced 100644
Binary files a/example of results/PL_family_WGS_fisher_1665057598/res_fisher.tsv.gz and b/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.tsv.gz differ
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.vcf.gz b/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..30fd59129bb063699b06aaf80dbfb098fd356209
Binary files /dev/null and b/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.vcf.gz differ
diff --git a/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.vcf.gz.tbi b/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.vcf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..957059b45acc0b21baba544750ac0cf2eff614a3
Binary files /dev/null and b/example_of_results/PL_family_WGS_fisher_1667491523/res_fisher.vcf.gz.tbi differ
diff --git a/fisher_for_vcf.config b/fisher_for_vcf.config
index 8605c2c85ea9a9e8557989974af30044b42ad4e8..d4520e818d361a67df9fe26ea0b241dbc1d5e5c9 100644
--- a/fisher_for_vcf.config
+++ b/fisher_for_vcf.config
@@ -16,18 +16,18 @@
 
 // variables exported to the main.nf environment. See https://www.nextflow.io/docs/latest/config.html#scope-env
 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" // vcf. Example: /pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz. Warning, if zipped (.gz) must be together with a .tbi file
+    sample_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz" // vcf. Example: "/pasteur/zeus/projets/p02/ghfc_wgs_zeus/WGS/Dyslexia/vcf/Dyslexia.gatk-vqsr.splitted.norm.vep.merged.vcf.gz". Warning, if zipped (.gz) must be together with a .tbi file. Another example: "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.gatk-vqsr.splitted.norm.vep.merged_first_10000.vcf.gz"
     ped_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.pedigree.txt" // pedigree
-    //ped_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" // pedigree
+    //ped_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/08002_bourgeron/dataset/Dyslexia.pedigree.txt" or /mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/Dyslexia.pedigree.txt
     chr_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
-    //chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
+    //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 = "chr1" // 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 = "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
     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 = 3 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
-    y_lim2 = 2 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
+    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"
     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"
 }
 
@@ -51,7 +51,7 @@ result_folder_name = "PL_family_WGS_fisher"
 //// slurm variables
 // see https://confluence.pasteur.fr/pages/viewpage.action?pageId=69304504
 queue = 'common,dedicated' // -p option of slurm. Example: queue = 'common,dedicated'. Example: queue = 'hubbioit'
-qos = '--qos=ultrafast' // --qos option of slurm. Example: qos= '--qos=fast'. Example: qos = '--qos=ultrafast'. Example: qos = '--qos=hubbioit'
+qos = '--qos=ultrafast' // --qos option of slurm. Example: qos= '--qos=fast'. Example: qos = '--qos=ultrafast'. Example: qos = '--qos=hubbioit'. Warning, qos = '--qos=normal' only works with queue = 'common', not queue = 'common,dedicated'
 add_options = ' ' // additional option of slurm. Example: addoptions = '--exclude=maestro-1101,maestro-1034' or add_options = ' ', add_options = '--time=70:00:00' (acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds"). See https://slurm.schedmd.com/sbatch.html#OPT_time for other options
 //// end slurm variables
 
diff --git a/fisher_for_vcf.nf b/fisher_for_vcf.nf
index 8ed1968facb72ad20142b55a8045d4005d818cfa..7dc461873ac10b128739271a4dc625b395e5c341 100644
--- a/fisher_for_vcf.nf
+++ b/fisher_for_vcf.nf
@@ -1,3 +1,4 @@
+nextflow.enable.dsl=1
 /*
 #########################################################################
 ##                                                                     ##
@@ -44,7 +45,7 @@ modules = params.modules // remove the dot -> can be used in bash scripts
 
 
 if(x_lim == 'whole' || (x_lim == 'region' && region == 'none')){ // for the miami plot
-    x_lim_val = "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"
+    x_lim_val = "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" // I have added both notations "chr23", "chr24", "chr25" or "chrY", "chrX", "chrM" because either one or the other can be used in a VCF file 
 }else if(x_lim == 'region'){
     x_lim_val = region
 }else{
@@ -59,7 +60,7 @@ if(x_lim == 'whole' || (x_lim == 'region' && region == 'none')){ // for the miam
 
 Channel.fromPath("${sample_path}", checkIfExists: false).into{vcf_ch1 ; vcf_ch2 ; vcf_ch3} // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
 if(region == 'none'){  // for combine below for parallelization of the fisher process
-    region_ch = Channel.from("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chr23", "chr24", "chr25", "chrY", "chrX", "chrM")
+    region_ch = Channel.from("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chr23", "chr24", "chr25", "chrY", "chrX", "chrM") // I have added both notations "chr23", "chr24", "chr25" or "chrY", "chrX", "chrM" because either one or the other can be used in a VCF file 
 }else{
     if(region =~ /,/){
         tempo = region.replaceAll(':.+,', ',')
@@ -117,11 +118,11 @@ if( ! bottom_y_column in String ){
 if( ! color_column in String ){
     error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID color_column PARAMETER IN nextflow.config FILE:\n${color_column}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
 }
-if( ! y_lim1 in Integer ){
-    error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim1 PARAMETER IN nextflow.config FILE:\n${y_lim1}\nMUST BE A SINGLE INTEGER\n\n========\n\n"
+if( ! y_lim1 in String ){
+    error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim1 PARAMETER IN nextflow.config FILE:\n${y_lim1}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
 }
-if( ! y_lim2 in Integer ){
-    error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim2 PARAMETER IN nextflow.config FILE:\n${y_lim2}\nMUST BE A SINGLE INTEGER\n\n========\n\n"
+if( ! y_lim2 in String ){
+    error "\n\n========\n\nERROR IN NEXTFLOW EXECUTION\n\nINVALID y_lim2 PARAMETER IN nextflow.config FILE:\n${y_lim2}\nMUST BE A SINGLE CHARACTER STRING\n\n========\n\n"
 }
 def file_exists5 = cute.exists()
 if( ! file_exists5){
@@ -131,6 +132,7 @@ if( ! file_exists5){
 // below : those variable are already used in the config file. Thus, to late to check them. And not possible to check inside the config file
 // system_exec
 // out_ini
+print("\n\nRESULT DIRECTORY: ${out_path}")
 print("\n\nWARNING: PARAMETERS ALREADY INTERPRETED IN THE .config FILE:")
 print("    system_exec: ${system_exec}")
 print("    out_path: ${out_path_ini}")
@@ -220,7 +222,12 @@ process fisher {
     script:
     """
     #!/bin/bash -ue
-    fisher_lod.py ${vcf} ${ped} "${region2}" ${vcf_info_field_titles} "${tsv_extra_fields}" "${vcf_csq_subfield_titles}" "fisher_report.txt"
+    if grep -Eq "FISHER" ${vcf_info_field_titles} ; then # does not work without [[]]
+        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})\\n\\n========\\n\\n"
+        exit 1
+    else
+        fisher_lod.py ${vcf} ${ped} "${region2}" ${vcf_info_field_titles} "${tsv_extra_fields}" ${vcf_csq_subfield_titles} "fisher_report.txt"
+    fi
     """
 }
 
@@ -297,9 +304,9 @@ process tsv2vcf {
         NR==1{
             print "##WARNING: 5 first names of the header of the initial file: "\$1" "\$2" "\$3" "\$4" "\$5"\\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" ;
-            print "##INFO=<FISHER=" ;
+            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: " ;
             for(i=6;i<=NF;i++){print \$i ; if(i < NF){print "|"}} ;
-            print ">\\n" ;
+            print "\"">\\n" ;
             print var1"\\n"
         }
         NR > 1{