Commit 5d4dba89 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

Warning: with resume, the figure 38 is not the good one taken -> problem with...

Warning: with resume, the figure 38 is not the good one taken -> problem with the cache. Otherwise, goalign added. Remains to create empty png from gogalign and to insert into the markdown
parent e26f44e6
......@@ -416,7 +416,7 @@ b$orient[b$orient == 0] <- "Forward"
b$orient[b$orient == 16] <- "Reverse"
# verifications right of Ori
fun_report(data = "\n\nOn the right of the Ori and the left of the ter:\n<br />Forward insertion = Leading (aka 0)\n<br />Reverse insertion = Lagging (aka 16)", output = report.rmd, path = "./", overwrite = FALSE)
fun_report(data = "\n\nOn the right of the Ori and the left of the ter:\n<br />Forward insertion = Leading (i.e., reads with FLAG=0 are leading strand)\n<br />Reverse insertion = Lagging (i.e., reads with FLAG=16 are lagging strand)", output = report.rmd, path = "./", overwrite = FALSE)
d <- b[b$Position > ori.center & b$Position < ter.center,]
options(scipen = 1000) # to avoid writing of scientific numbers in tables, see https://stackoverflow.com/questions/3978266/number-format-writing-1e-5-instead-of-0-00001
write.table(as.data.frame.matrix(addmargins(table(d[, c("fork", "orient")]))), file = paste0("./table1.txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t")
......@@ -443,7 +443,7 @@ fun_report(data = tempo.cat, output = report.rmd, path = "./", overwrite = FALSE
# verifications left of Ori
fun_report(data = "\n\nOn the left of the Ori and the right of the ter:\n<br />Forward insertion = Lagging (aka 16)\n<br />Reverse insertion = Leading (aka 0)", output = report.rmd, path = "./", overwrite = FALSE)
fun_report(data = "\n\nOn the left of the Ori and the right of the ter:\n<br />Forward insertion = Lagging (i.e., reads with FLAG=0 are lagging strand)\n<br />Reverse insertion = Leading (i.e., reads with FLAG=16 are lagging strand)", output = report.rmd, path = "./", overwrite = FALSE)
e<- b[b$Position < ori.center | b$Position > ter.center,]
options(scipen = 1000) # to avoid writing of scientific numbers in tables, see https://stackoverflow.com/questions/3978266/number-format-writing-1e-5-instead-of-0-00001
write.table(as.data.frame.matrix(addmargins(table(e[, c("fork", "orient")]))), file = paste0("./table3.txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t")
......
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
3 c6/b5a87f 233 report1 COMPLETED 0 2022-03-31 09:31:45.419 1.6s 18ms 5.2% 0 0 104.6 KB 694 B
1 b0/6d17f5 202 init COMPLETED 0 2022-03-31 09:31:45.385 1.7s 11ms 6.0% 0 0 104.2 KB 676 B
5 6a/41b53f 357 backup COMPLETED 0 2022-03-31 09:31:45.602 1.6s 14ms 5.6% 0 0 104.4 KB 511 B
2 60/ec2927 181 Nremove (1) COMPLETED 0 2022-03-31 09:31:45.348 1.9s 438ms 47.9% 11.8 MB 70.6 MB 16.8 MB 14.5 MB
6 21/fc97ed 394 workflowVersion COMPLETED 0 2022-03-31 09:31:45.630 2.4s 962ms 12.1% 4.8 MB 38.4 MB 133.5 KB 2.1 KB
7 f6/1888ae 1135 trim (1) COMPLETED 0 2022-03-31 09:31:47.349 3.3s 2.2s 42.6% 38.8 MB 5.6 GB 16.4 MB 12 MB
10 90/fb9dd7 1715 kraken (1) COMPLETED 0 2022-03-31 09:31:50.658 167ms 8ms 64.0% 0 0 151 KB 231 B
8 21/3c2e17 1739 fivep_filtering (1) COMPLETED 0 2022-03-31 09:31:50.692 2.9s 1.9s 26.7% 9.6 MB 61.4 MB 28 MB 15.3 MB
12 fc/7433af 2536 cutoff (1) COMPLETED 0 2022-03-31 09:31:53.762 2s 712ms 18.6% 9.6 MB 61.3 MB 7 MB 3.9 MB
9 97/f9aa8f 1807 fastqc1 (1) COMPLETED 0 2022-03-31 09:31:50.716 7.6s 6.6s 65.4% 189.7 MB 3.1 GB 13.9 MB 1.2 MB
11 59/c4b7ed 2509 fastqc2 (1) COMPLETED 0 2022-03-31 09:31:53.700 6.2s 5.1s 62.5% 143.5 MB 3.1 GB 12.2 MB 1.2 MB
4 12/9d071e 335 motif COMPLETED 0 2022-03-31 09:31:45.576 18.4s 17s 47.3% 209.1 MB 407.3 MB 48.8 MB 39.7 MB
13 45/ae26f7 3940 plot_fivep_filtering_stat (1) COMPLETED 0 2022-03-31 09:32:03.942 13.8s 12.9s 52.6% 181.7 MB 427 MB 19.5 MB 812.8 KB
15 a6/6f3471 4649 bowtie2 (1) COMPLETED 0 2022-03-31 09:32:17.704 4.3s 3.4s 57.9% 112.8 MB 239.5 MB 35 MB 16.2 MB
16 a5/b0a651 5106 Q20 (1) COMPLETED 0 2022-03-31 09:32:22.078 1.5s 363ms 18.7% 5.8 MB 42.8 MB 3.2 MB 2.2 MB
19 8b/ffe2b3 5641 no_soft_clipping (1) COMPLETED 0 2022-03-31 09:32:24.630 1.5s 270ms 13.4% 3.4 MB 38.4 MB 2.1 MB 1.5 MB
20 c7/508005 5663 duplicate_removal (1) COMPLETED 0 2022-03-31 09:32:24.650 2.9s 1.8s 26.6% 6.4 MB 38.4 MB 12.9 MB 6.6 MB
22 f0/f80457 6730 insertion (1) COMPLETED 0 2022-03-31 09:32:28.515 1.6s 521ms 19.1% 9.2 MB 65.6 MB 2.5 MB 1.7 MB
24 91/41d9a8 6736 insertion (2) COMPLETED 0 2022-03-31 09:32:28.533 1.7s 574ms 20.4% 7.8 MB 65.6 MB 3 MB 2.2 MB
18 bc/6f4ebe 5139 multiQC COMPLETED 0 2022-03-31 09:32:22.098 8.4s 8s 40.8% 71.9 MB 82.3 MB 28.3 MB 2.3 MB
14 be/6a3fa2 5068 plot_read_length (1) COMPLETED 0 2022-03-31 09:32:22.034 14.8s 13.9s 58.0% 181.9 MB 417.7 MB 20 MB 712.6 KB
17 db/29996f 7537 coverage (1) COMPLETED 0 2022-03-31 09:32:36.842 1.6s 629ms 17.9% 5.1 MB 44.6 MB 479.8 KB 91 KB
21 ce/89bb59 7693 coverage (2) COMPLETED 0 2022-03-31 09:32:38.401 1.3s 542ms 20.8% 5.1 MB 44.6 MB 335.2 KB 82.4 KB
23 c7/7907eb 7847 coverage (3) COMPLETED 0 2022-03-31 09:32:39.731 1.4s 545ms 19.1% 5.1 MB 44.6 MB 310.4 KB 82.1 KB
25 44/a1b906 7998 final_insertion_files (1) COMPLETED 0 2022-03-31 09:32:41.142 6.4s 5.7s 41.2% 134.1 MB 332.2 MB 18.4 MB 318.2 KB
31 6a/9443e7 8456 report3 (1) COMPLETED 0 2022-03-31 09:32:47.564 971ms 29ms 13.3% 0 0 176.9 KB 535 B
26 44/c4b2cf 8432 final_insertion_files (2) COMPLETED 0 2022-03-31 09:32:47.541 6.5s 5.7s 41.5% 135.1 MB 333.3 MB 18.4 MB 318.2 KB
27 cf/b9fba8 8998 plot_coverage (1) COMPLETED 0 2022-03-31 09:32:54.043 16s 15.3s 47.0% 146 MB 391.7 MB 19.5 MB 460.6 KB
28 e8/72aa08 9711 plot_coverage (2) COMPLETED 0 2022-03-31 09:33:10.063 12.5s 11.8s 58.6% 224.6 MB 436.6 MB 19.5 MB 454.7 KB
29 a1/4547ae 10417 plot_coverage (3) COMPLETED 0 2022-03-31 09:33:22.594 12.8s 12s 58.3% 220.4 MB 431.4 MB 19.5 MB 455.3 KB
30 95/3650da 11124 seq_around_insertion (1) COMPLETED 0 2022-03-31 09:33:35.366 6.6s 5.9s 42.7% 133.8 MB 331.7 MB 18.4 MB 229.5 KB
32 6b/1a0ec6 11558 random_insertion (1) COMPLETED 0 2022-03-31 09:33:42.025 10.7s 9.9s 53.8% 367.8 MB 577.1 MB 31.2 MB 1.2 MB
33 30/f186d8 12208 seq_around_insertion (2) COMPLETED 0 2022-03-31 09:33:52.713 6.7s 6s 42.0% 133.5 MB 331.6 MB 18.4 MB 163.4 KB
34 d5/add756 12654 dup_insertion_and_logo (1) COMPLETED 0 2022-03-31 09:33:59.434 13.1s 12.4s 60.0% 176.3 MB 387.8 MB 17.8 MB 526.6 KB
35 0f/010866 13383 extract_seq (1) COMPLETED 0 2022-03-31 09:34:12.542 1.7s 815ms 20.1% 5.9 MB 50.4 MB 9.1 MB 4.5 MB
38 ea/138194 13651 base_freq (1) COMPLETED 0 2022-03-31 09:34:14.293 1.4s 96ms 9.9% 0 0 279.8 KB 16.8 KB
41 5d/a11b6c 13590 base_freq (4) COMPLETED 0 2022-03-31 09:34:14.250 1.6s 99ms 12.0% 0 0 282.1 KB 19 KB
40 32/dba095 13693 base_freq (3) COMPLETED 0 2022-03-31 09:34:14.315 1.6s 99ms 11.0% 0 0 282.7 KB 19.7 KB
39 04/a23943 13742 base_freq (2) COMPLETED 0 2022-03-31 09:34:14.337 1.6s 101ms 11.1% 0 0 281.9 KB 18.9 KB
36 07/07d7b0 13577 plot_insertion (1) COMPLETED 0 2022-03-31 09:34:14.226 3m 38s 3m 37s 32.7% 1.1 GB 1.3 GB 59.1 MB 17.7 MB
37 18/3237c2 18231 extract_seq (2) COMPLETED 0 2022-03-31 09:37:52.165 1.4s 468ms 19.7% 5.9 MB 50.4 MB 9 MB 4.5 MB
49 0d/8a0c99 18454 base_freq (8) COMPLETED 0 2022-03-31 09:37:53.563 1.5s 41ms 11.3% 0 0 180.5 KB 7 KB
47 0c/b8dd30 18514 base_freq (6) COMPLETED 0 2022-03-31 09:37:53.610 1.5s 38ms 11.0% 0 0 178.7 KB 5.1 KB
48 e6/ef7c36 18567 base_freq (7) COMPLETED 0 2022-03-31 09:37:53.629 1.7s 41ms 10.9% 0 0 176.4 KB 2.8 KB
46 44/4501dd 18603 base_freq (5) COMPLETED 0 2022-03-31 09:37:53.648 1.7s 50ms 8.0% 0 0 182.5 KB 8.9 KB
50 d6/eb7d31 19171 report2 COMPLETED 0 2022-03-31 09:37:56.354 960ms 22ms 9.3% 0 0 131.9 KB 2 KB
42 49/87dc82 18440 logo (1) COMPLETED 0 2022-03-31 09:37:53.542 12.2s 11.2s 27.4% 184.9 MB 395.7 MB 15.1 MB 1023.2 KB
43 85/acf092 19803 logo (2) COMPLETED 0 2022-03-31 09:38:05.751 7.3s 6.6s 45.7% 183.1 MB 394 MB 15.1 MB 904.1 KB
44 6a/37a6b6 20291 logo (3) COMPLETED 0 2022-03-31 09:38:13.101 7.3s 6.6s 45.0% 182.6 MB 393.6 MB 15.1 MB 894.6 KB
45 3e/6f606f 20781 logo (4) COMPLETED 0 2022-03-31 09:38:20.371 7.2s 6.5s 46.0% 184.4 MB 393.4 MB 15.1 MB 874 KB
51 47/e9041b 21265 global_logo (1) COMPLETED 0 2022-03-31 09:38:27.562 7.5s 6.8s 47.9% 179.6 MB 390.3 MB 15.1 MB 867.7 KB
52 7c/d7021a 21760 global_logo (2) COMPLETED 0 2022-03-31 09:38:35.091 7.5s 6.9s 48.6% 181.3 MB 392.6 MB 15.1 MB 988 KB
53 0b/7d3032 22259 print_report (1) COMPLETED 0 2022-03-31 09:38:42.977 11s 10.3s 39.8% 222.7 MB 1 TB 44.2 MB 19.9 MB
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