Commit d4960087 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

release v8.3.0: Small bug removed: now same orientation plotted in the CDS plots

parent 711b04ce
......@@ -209,6 +209,11 @@ Gitlab developers
## WHAT'S NEW IN
### v8.3.0
1) Small bug removed: now same orientation plotted in the CDS plots
### v8.2.0
1) All the problems should be solved in this version
......
......@@ -130,10 +130,6 @@ rm(tempo.cat)
################################ end Test
################################ Recording of the initial parameters
......@@ -864,16 +860,15 @@ if(tss_path != "NULL"){
ini.date <- Sys.time()
ini.time <- as.numeric(ini.date) # time of process begin, converted into
tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
fun_report(data = paste0("\n", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
cat("\n", tempo.cat, "\n")
thread.nb = task.cpus # detect the number of threads
tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
fun_report(data = paste0("\n ", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
cat("\n ", tempo.cat, "\n")
Clust <- parallel::makeCluster(thread.nb, outfile = paste0("./insertion_site_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
tempo.cat <- paste0("SPLIT OF TEST NUMBERS IN PARALLELISATION:")
fun_report(data = paste0("\n ", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
cat(tempo.cat)
cluster.list <- parallel::clusterSplit(Clust, 1:nrow(obs.rd.freq)) # split the number of rows of obs.rd.freq according to the number of cluster
fun_report(data = str(cluster.list), output = log, path = "./", overwrite = FALSE)
str(cluster.list)
fun_report(data = paste0("\n"), output = log, path = "./", overwrite = FALSE)
print.count <- 1000
paral.output.list <- parallel::clusterApply( # paral.output.list is a list made of thread.nb compartments, each made of n / thread.nb (mat theo column number) compartment. Each compartment receive the corresponding results of fun_permut(), i.e., data (permuted mat1.perm), warning message, cor (final correlation) and count (number of permutations)
......@@ -1000,6 +995,7 @@ if(tss_path != "NULL"){
# creation of the new column same_orient
final$orient <- toupper(final$orient)
final <- data.frame(final, same_orient = final$tss.orient == final$orient)
final$same_orient[final$same_orient == TRUE] <- "SAME"
final$same_orient[final$same_orient == FALSE] <- "OPPOSITE"
......@@ -1028,16 +1024,15 @@ if(tss_path != "NULL"){
ini.date <- Sys.time()
ini.time <- as.numeric(ini.date) # time of process begin, converted into
tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
fun_report(data = paste0("\n", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
cat("\n", tempo.cat, "\n")
thread.nb = task.cpus # detect the number of threads
tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
fun_report(data = paste0("\n ", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
cat("\n ", tempo.cat, "\n")
Clust <- parallel::makeCluster(thread.nb, outfile = paste0("./", tolower(i0), ".insertion_site_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
tempo.cat <- paste0("SPLIT OF LOOP NUMBERS IN PARALLELISATION:")
cat(tempo.cat)
fun_report(data = paste0("\n ", tempo.cat, "\n"), output = log, path = "./", overwrite = FALSE)
cluster.list <- parallel::clusterSplit(Clust, 1:length(gene.loop)) # split the number of rows of obs.rd.freq according to the number of cluster
fun_report(data = str(cluster.list), output = log, path = "./", overwrite = FALSE) # using print(str()) add a NULL below the result
str(cluster.list) # using print(str()) add a NULL below the result
fun_report(data = paste0("\n"), output = log, path = "./", overwrite = FALSE)
paral.output.list <- parallel::clusterApply( # paral.output.list is a list made of thread.nb compartments, each made of n / thread.nb (mat theo column number) compartment. Each compartment receive the corresponding results of fun_permut(), i.e., data (permuted mat1.perm), warning message, cor (final correlation) and count (number of permutations)
cl = Clust,
......
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task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
1 56/70aa49 32343 init COMPLETED 0 2022-04-08 11:28:01.027 1.5s 12ms 9.1% 0 0 104.1 KB 670 B
3 2b/f81796 32381 report1 COMPLETED 0 2022-04-08 11:28:01.061 1.6s 17ms 5.6% 0 0 104.5 KB 688 B
2 b7/6cfea3 32317 Nremove (1) COMPLETED 0 2022-04-08 11:28:00.994 1.8s 413ms 51.3% 11.9 MB 70.6 MB 16.8 MB 14.5 MB
5 3f/8fb58f 32472 backup COMPLETED 0 2022-04-08 11:28:01.257 1.6s 14ms 5.5% 0 0 104.3 KB 505 B
6 56/5a693d 32501 workflowVersion COMPLETED 0 2022-04-08 11:28:01.290 2.1s 719ms 12.7% 5 MB 38.4 MB 133.5 KB 2.1 KB
7 5e/34dde3 718 trim (1) COMPLETED 0 2022-04-08 11:28:02.884 2.9s 2s 44.3% 38.4 MB 5.5 GB 16.4 MB 12 MB
10 19/89298f 1409 kraken (1) COMPLETED 0 2022-04-08 11:28:05.865 91ms 9ms 53.3% 0 0 150.9 KB 225 B
9 64/cafef9 1492 fivep_filtering (1) COMPLETED 0 2022-04-08 11:28:05.911 2.8s 1.7s 25.2% 12.1 MB 73.1 MB 28 MB 15.3 MB
11 f6/e8c39a 2228 cutoff (1) COMPLETED 0 2022-04-08 11:28:08.785 1.7s 686ms 16.7% 9.8 MB 61.3 MB 7 MB 3.9 MB
8 60/0b4e8e 1425 fastqc1 (1) COMPLETED 0 2022-04-08 11:28:05.884 5.8s 4.9s 77.2% 188 MB 3.1 GB 13.9 MB 1.2 MB
12 f6/59584a 2202 fastqc2 (1) COMPLETED 0 2022-04-08 11:28:08.765 6.9s 6s 52.6% 149.3 MB 3.1 GB 12.3 MB 1.2 MB
15 ca/4fd36f 3087 bowtie2 (1) COMPLETED 0 2022-04-08 11:28:11.542 4.6s 3.6s 54.0% 115 MB 239.5 MB 35 MB 16.2 MB
4 6e/720532 661 motif COMPLETED 0 2022-04-08 11:28:02.784 15.1s 14.3s 51.6% 193.9 MB 317.8 MB 47.6 MB 39.7 MB
16 1e/b5b2c2 4085 Q20 (1) COMPLETED 0 2022-04-08 11:28:17.131 1.4s 379ms 21.0% 6.7 MB 43.3 MB 3.2 MB 2.2 MB
20 06/536e8c 4611 no_soft_clipping (1) COMPLETED 0 2022-04-08 11:28:19.552 1.3s 287ms 15.3% 3.4 MB 38.4 MB 2.1 MB 1.5 MB
19 99/c5a8bc 4635 duplicate_removal (1) COMPLETED 0 2022-04-08 11:28:19.573 2.9s 1.8s 25.7% 7.3 MB 53 MB 12.9 MB 6.6 MB
18 bb/84a66e 4111 multiQC COMPLETED 0 2022-04-08 11:28:17.150 7.7s 7s 42.9% 64.6 MB 75 MB 28.3 MB 2.3 MB
23 73/2e1177 5700 insertion (1) COMPLETED 0 2022-04-08 11:28:23.441 1.5s 476ms 21.3% 9 MB 65.6 MB 2.5 MB 1.7 MB
24 18/5cf91a 5725 insertion (2) COMPLETED 0 2022-04-08 11:28:23.460 1.6s 534ms 20.9% 9.1 MB 65.6 MB 3 MB 2.2 MB
13 c6/2d6f62 4305 plot_fivep_filtering_stat (1) COMPLETED 0 2022-04-08 11:28:17.854 12.1s 11.2s 57.2% 210.6 MB 346.8 MB 18.2 MB 792.5 KB
14 74/84292e 6567 plot_read_length (1) COMPLETED 0 2022-04-08 11:28:29.922 12.1s 11.4s 64.3% 276.7 MB 413.2 MB 18.7 MB 691.5 KB
17 74/cf8666 7273 coverage (1) COMPLETED 0 2022-04-08 11:28:42.009 1.4s 597ms 20.5% 5.2 MB 44.6 MB 479.7 KB 91 KB
21 d7/6be0b0 7432 coverage (2) COMPLETED 0 2022-04-08 11:28:43.420 1.4s 591ms 18.4% 4.9 MB 44.6 MB 335.1 KB 82.4 KB
22 d1/7ba1c0 7591 coverage (3) COMPLETED 0 2022-04-08 11:28:44.870 1.5s 612ms 17.3% 5 MB 44.6 MB 310.3 KB 82.1 KB
25 13/11a8a0 7747 final_insertion_files (1) COMPLETED 0 2022-04-08 11:28:46.390 5.6s 4.8s 41.8% 122 MB 246.8 MB 17.2 MB 269.2 KB
31 b9/3a6a38 8160 report3 (1) COMPLETED 0 2022-04-08 11:28:51.992 1.1s 31ms 12.0% 0 0 176.8 KB 529 B
26 4b/3f2ab7 8137 final_insertion_files (2) COMPLETED 0 2022-04-08 11:28:51.973 5.8s 4.9s 41.2% 121.7 MB 246.8 MB 17.2 MB 278.8 KB
27 09/2728b8 8647 plot_coverage (1) COMPLETED 0 2022-04-08 11:28:57.751 11s 10.3s 58.0% 219.8 MB 358.8 MB 18.3 MB 440.1 KB
28 09/225c9f 9311 plot_coverage (2) COMPLETED 0 2022-04-08 11:29:08.790 10.8s 10.1s 58.7% 217.4 MB 355.3 MB 18.3 MB 434.3 KB
29 8d/6dfd6b 9965 plot_coverage (3) COMPLETED 0 2022-04-08 11:29:19.640 10.5s 9.8s 60.0% 218.9 MB 355.4 MB 18.3 MB 434.9 KB
32 3e/cc8b31 10618 random_insertion (1) COMPLETED 0 2022-04-08 11:29:30.150 8.8s 8.1s 56.7% 351.5 MB 487.6 MB 30 MB 1.2 MB
30 1e/28c3c8 11161 seq_around_insertion (1) COMPLETED 0 2022-04-08 11:29:38.950 5.1s 4.4s 45.0% 122.3 MB 247.7 MB 17.2 MB 208.4 KB
33 23/cdd1bb 11553 seq_around_insertion (2) COMPLETED 0 2022-04-08 11:29:44.091 5.1s 4.4s 44.3% 122.5 MB 248 MB 17.2 MB 229.8 KB
34 a5/4eef93 11932 dup_insertion_and_logo (1) COMPLETED 0 2022-04-08 11:29:49.221 10.9s 10.2s 63.8% 235.4 MB 371.9 MB 16.6 MB 506.4 KB
35 bc/c21047 12606 plot_insertion (1) COMPLETED 0 2022-04-08 11:30:00.161 3m 54s 3m 54s 36.4% 398.8 MB 550.1 MB 44.7 MB 22.2 MB
36 9d/01ac1e 18846 extract_seq (1) COMPLETED 0 2022-04-08 11:33:54.640 1.7s 809ms 18.1% 5.6 MB 50.2 MB 9.1 MB 4.5 MB
38 5a/1922ff 19110 base_freq (1) COMPLETED 0 2022-04-08 11:33:56.398 1.4s 90ms 9.6% 0 0 279.7 KB 16.8 KB
40 fa/34dfa7 19135 base_freq (3) COMPLETED 0 2022-04-08 11:33:56.419 1.5s 101ms 9.9% 0 0 282.6 KB 19.7 KB
41 74/093e9a 19166 base_freq (4) COMPLETED 0 2022-04-08 11:33:56.439 1.6s 98ms 14.7% 0 0 282 KB 19 KB
39 e0/6c655b 19221 base_freq (2) COMPLETED 0 2022-04-08 11:33:56.460 1.6s 97ms 11.6% 0 0 281.8 KB 18.9 KB
37 c4/7341ef 19059 extract_seq (2) COMPLETED 0 2022-04-08 11:33:56.323 2.3s 1.2s 16.4% 5 MB 50.2 MB 9.1 MB 4.6 MB
49 db/d4ec97 19866 base_freq (7) COMPLETED 0 2022-04-08 11:33:58.697 1.5s 127ms 11.0% 0 0 324 KB 23.7 KB
50 07/34b3f1 19901 base_freq (8) COMPLETED 0 2022-04-08 11:33:58.716 1.7s 121ms 13.5% 0 0 325.8 KB 25.5 KB
48 b8/81db80 19931 base_freq (6) COMPLETED 0 2022-04-08 11:33:58.734 1.7s 117ms 10.8% 0 0 323.7 KB 23.3 KB
46 80/c2a36f 19798 goalign (1) COMPLETED 0 2022-04-08 11:33:58.649 1.9s 840ms 16.4% 3 MB 14 MB 622.2 KB 796.1 KB
47 6d/191d06 20474 base_freq (5) COMPLETED 0 2022-04-08 11:34:00.242 1s 70ms 14.8% 0 0 323.4 KB 23 KB
52 da/fe4ca9 20753 report2 COMPLETED 0 2022-04-08 11:34:02.250 873ms 33ms 13.1% 0 0 131.8 KB 2 KB
42 76/022b07 19776 logo (1) COMPLETED 0 2022-04-08 11:33:58.628 7s 5.9s 46.1% 171.8 MB 309.9 MB 13.8 MB 1002.7 KB
43 56/c2624f 21056 logo (2) COMPLETED 0 2022-04-08 11:34:05.599 6s 5.3s 50.5% 166.5 MB 305.7 MB 13.8 MB 873.9 KB
45 7f/a09e0c 21468 logo (4) COMPLETED 0 2022-04-08 11:34:11.610 6.1s 5.3s 50.2% 170 MB 306.8 MB 13.8 MB 853.1 KB
44 fc/9004da 21899 logo (3) COMPLETED 0 2022-04-08 11:34:17.680 6s 5.3s 50.4% 169.3 MB 307.6 MB 13.8 MB 883.3 KB
51 2d/e3eb2c 22332 global_logo (1) COMPLETED 0 2022-04-08 11:34:23.731 6.5s 5.8s 53.1% 170 MB 307.2 MB 13.8 MB 846.9 KB
53 7f/17ad1d 22769 global_logo (2) COMPLETED 0 2022-04-08 11:34:30.270 6.4s 5.7s 53.9% 171.2 MB 308.4 MB 13.8 MB 922.1 KB
54 97/e12abb 23212 print_report (1) COMPLETED 0 2022-04-08 11:34:37.259 10.2s 9.4s 44.6% 261.2 MB 1 TB 50.9 MB 25.6 MB
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