SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28 Output file will be GZIP compressed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4479.26 s (23 µs/read; 2.61 M reads/minute). === Summary === Total reads processed: 194,821,663 Reads with adapters: 22,011,384 (11.3%) Reads written (passing filters): 194,821,663 (100.0%) Total basepairs processed: 18,329,414,001 bp Quality-trimmed: 4,444,384 bp (0.0%) Total written (filtered): 18,054,741,769 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 22011384 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 24.7% C: 4.8% G: 0.0% T: 70.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13318172 48705415.8 0 13318172 2 4043535 12176353.9 0 4043535 3 883652 3044088.5 0 883652 4 256064 761022.1 0 256064 5 79698 190255.5 0 79698 6 22627 47563.9 0 22627 7 9771 11891.0 0 9771 8 7035 2972.7 0 7035 9 6780 743.2 0 6780 10 12942 185.8 1 6323 6619 11 11367 46.4 1 5535 5832 12 9608 11.6 1 4990 4618 13 8292 2.9 1 4292 4000 14 7434 0.7 1 3838 3596 15 6674 0.2 1 3440 3234 16 5606 0.0 1 2939 2667 17 4419 0.0 1 2376 2043 18 3617 0.0 1 2252 1365 19 3270 0.0 1 2091 1179 20 5224 0.0 2 2184 1120 1920 21 4782 0.0 2 2091 1075 1616 22 4380 0.0 2 1935 981 1464 23 3975 0.0 2 1710 987 1278 24 3912 0.0 2 1787 933 1192 25 3468 0.0 2 1677 818 973 26 3118 0.0 2 1475 758 885 27 3044 0.0 2 1452 734 858 28 2688 0.0 2 1442 722 524 29 2499 0.0 2 1364 630 505 30 3310 0.0 3 1244 713 463 890 31 3167 0.0 3 1221 629 516 801 32 3157 0.0 3 1225 664 480 788 33 3156 0.0 3 1235 636 507 778 34 2940 0.0 3 1102 658 475 705 35 2887 0.0 3 1085 620 480 702 36 2838 0.0 3 1179 607 473 579 37 2680 0.0 3 1166 559 404 551 38 2465 0.0 3 1123 553 391 398 39 2444 0.0 3 1129 573 372 370 40 2990 0.0 4 1075 536 357 350 672 41 3019 0.0 4 1049 594 421 374 581 42 2935 0.0 4 1067 563 375 321 609 43 2936 0.0 4 1016 585 386 359 590 44 2807 0.0 4 988 551 373 341 554 45 2712 0.0 4 1012 480 350 337 533 46 2655 0.0 4 1016 539 367 308 425 47 2678 0.0 4 1026 605 345 271 431 48 2863 0.0 4 1119 645 446 336 317 49 6170 0.0 4 2262 1348 1061 870 629 50 6669 0.0 5 2308 1425 1040 779 627 490 51 5168 0.0 5 2320 1024 687 499 340 298 52 4526 0.0 5 2077 934 569 427 292 227 53 4229 0.0 5 2113 894 497 329 219 177 54 3995 0.0 5 2164 769 452 289 170 151 55 3770 0.0 5 2149 717 393 246 147 118 56 3725 0.0 5 2209 682 341 215 152 126 57 4213 0.0 5 2806 677 312 186 143 89 58 4897 0.0 5 3642 573 296 184 114 88 59 4668 0.0 5 3542 532 253 163 101 77 60 3031 0.0 5 2007 467 260 143 94 60 61 3046 0.0 5 2056 495 227 145 71 52 62 3366 0.0 5 2458 448 212 105 88 55 63 4356 0.0 5 3505 424 188 125 71 43 64 6120 0.0 5 5247 449 186 104 86 48 65 3134 0.0 5 2163 433 284 137 74 43 66 3736 0.0 5 2868 448 214 104 59 43 67 3038 0.0 5 2298 412 159 87 49 33 68 3472 0.0 5 2706 398 188 90 53 37 69 4241 0.0 5 3480 413 171 78 57 42 70 8174 0.0 5 7442 411 145 91 50 35 71 19775 0.0 5 19014 467 140 71 53 30 72 121068 0.0 5 120214 553 143 74 44 40 73 238161 0.0 5 237330 502 150 80 51 48 74 1778702 0.0 5 1777903 465 151 100 52 31 75 82657 0.0 5 82020 346 142 70 51 28 76 63529 0.0 5 62968 319 111 69 37 25 77 374472 0.0 5 373944 292 110 69 31 26 78 29760 0.0 5 29287 248 118 56 35 16 79 212697 0.0 5 212210 244 106 68 38 31 80 46691 0.0 5 46277 212 103 52 26 21 81 26170 0.0 5 25753 206 85 66 37 23 82 73137 0.0 5 72770 172 84 53 27 31 83 7384 0.0 5 7000 163 99 57 44 21 84 29497 0.0 5 29086 213 87 55 31 25 85 6586 0.0 5 6262 162 62 39 38 23 86 963 0.0 5 637 144 85 40 32 25 87 932 0.0 5 626 140 69 49 34 14 88 803 0.0 5 521 117 64 42 30 29 89 739 0.0 5 484 112 57 42 23 21 90 676 0.0 5 442 100 56 31 22 25 91 701 0.0 5 472 96 51 43 24 15 92 552 0.0 5 350 83 43 36 26 14 93 571 0.0 5 361 85 46 34 27 18 94 551 0.0 5 332 90 57 24 30 18 95 510 0.0 5 329 65 41 40 23 12 96 414 0.0 5 254 59 39 27 19 16 97 442 0.0 5 270 66 43 33 18 12 98 413 0.0 5 253 55 36 24 29 16 99 344 0.0 5 205 45 43 18 18 15 100 292 0.0 5 194 31 26 20 9 12 101 297 0.0 5 193 48 22 17 11 6 102 259 0.0 5 184 29 16 13 9 8 103 232 0.0 5 155 28 16 12 15 6 104 195 0.0 5 123 22 18 17 9 6 105 154 0.0 5 107 16 15 3 5 8 106 159 0.0 5 102 19 10 10 6 12 107 131 0.0 5 84 13 10 5 11 8 108 125 0.0 5 87 8 7 6 4 13 109 109 0.0 5 84 9 6 1 1 8 110 82 0.0 5 56 11 5 5 2 3 111 63 0.0 5 41 5 4 6 5 2 112 55 0.0 5 41 4 5 1 1 3 113 43 0.0 5 30 6 0 3 0 4 114 62 0.0 5 42 7 2 3 2 6 115 193 0.0 5 179 9 1 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz ============================================= 194821663 sequences processed in total