SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_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_3_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4187.98 s (22 µs/read; 2.70 M reads/minute). === Summary === Total reads processed: 188,375,666 Reads with adapters: 21,487,316 (11.4%) Reads written (passing filters): 188,375,666 (100.0%) Total basepairs processed: 17,824,771,638 bp Quality-trimmed: 3,215,006 bp (0.0%) Total written (filtered): 17,516,630,527 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21487316 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: 26.4% C: 4.8% G: 0.0% T: 68.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12641085 47093916.5 0 12641085 2 3819940 11773479.1 0 3819940 3 818216 2943369.8 0 818216 4 234891 735842.4 0 234891 5 70824 183960.6 0 70824 6 20278 45990.2 0 20278 7 9122 11497.5 0 9122 8 6477 2874.4 0 6477 9 6440 718.6 0 6440 10 11606 179.6 1 5859 5747 11 10276 44.9 1 5251 5025 12 8714 11.2 1 4548 4166 13 7477 2.8 1 3942 3535 14 6748 0.7 1 3522 3226 15 5893 0.2 1 3045 2848 16 5158 0.0 1 2800 2358 17 4001 0.0 1 2221 1780 18 3396 0.0 1 2200 1196 19 3084 0.0 1 1996 1088 20 4649 0.0 2 2053 1006 1590 21 4154 0.0 2 1972 921 1261 22 3873 0.0 2 1864 897 1112 23 3765 0.0 2 1909 847 1009 24 3677 0.0 2 1753 895 1029 25 3324 0.0 2 1662 843 819 26 2905 0.0 2 1452 687 766 27 2911 0.0 2 1528 671 712 28 2553 0.0 2 1450 601 502 29 2473 0.0 2 1370 623 480 30 3100 0.0 3 1282 612 489 717 31 2966 0.0 3 1305 575 443 643 32 2839 0.0 3 1181 588 424 646 33 2909 0.0 3 1277 570 422 640 34 2776 0.0 3 1161 573 428 614 35 2830 0.0 3 1144 599 476 611 36 2520 0.0 3 1088 506 388 538 37 2546 0.0 3 1152 542 375 477 38 2348 0.0 3 1146 547 339 316 39 2384 0.0 3 1130 525 376 353 40 2945 0.0 4 1108 556 390 352 539 41 2746 0.0 4 1008 477 391 352 518 42 2694 0.0 4 1020 504 369 331 470 43 2722 0.0 4 1001 515 380 378 448 44 2565 0.0 4 906 504 334 326 495 45 2553 0.0 4 1037 464 352 300 400 46 2479 0.0 4 1013 500 315 289 362 47 2509 0.0 4 1076 503 329 253 348 48 2846 0.0 4 1222 632 431 283 278 49 5862 0.0 4 2461 1342 887 653 519 50 6105 0.0 5 2396 1308 868 617 515 401 51 4688 0.0 5 2494 876 527 355 246 190 52 3964 0.0 5 2252 729 399 270 180 134 53 3763 0.0 5 2275 687 319 209 153 120 54 3657 0.0 5 2311 619 333 180 118 96 55 3390 0.0 5 2176 557 308 169 105 75 56 3641 0.0 5 2560 487 271 151 111 61 57 4177 0.0 5 3173 476 248 114 101 65 58 4958 0.0 5 4010 468 238 130 74 38 59 4573 0.0 5 3708 422 200 105 86 52 60 2904 0.0 5 2106 408 188 94 66 42 61 2926 0.0 5 2181 385 163 99 61 37 62 3283 0.0 5 2613 352 142 81 61 34 63 4465 0.0 5 3818 361 139 60 46 41 64 6007 0.0 5 5330 376 142 79 45 35 65 3203 0.0 5 2450 344 227 102 50 30 66 3882 0.0 5 3172 389 189 58 50 24 67 3282 0.0 5 2631 366 131 79 53 22 68 3709 0.0 5 3107 348 127 69 37 21 69 4833 0.0 5 4191 410 109 62 41 20 70 10036 0.0 5 9436 376 120 57 30 17 71 26300 0.0 5 25603 441 137 62 28 29 72 161602 0.0 5 160850 514 125 66 32 15 73 313026 0.0 5 312367 439 121 57 22 20 74 2036504 0.0 5 2035846 442 108 52 41 15 75 90984 0.0 5 90513 287 94 48 22 20 76 81294 0.0 5 80829 273 92 52 28 20 77 406407 0.0 5 405997 246 75 37 32 20 78 39317 0.0 5 38952 213 68 47 21 16 79 241697 0.0 5 241343 184 91 39 23 17 80 52913 0.0 5 52567 180 68 56 25 17 81 32905 0.0 5 32580 185 61 36 28 15 82 83320 0.0 5 83028 157 50 43 27 15 83 7092 0.0 5 6801 149 60 36 25 21 84 22662 0.0 5 22392 152 64 28 17 9 85 3825 0.0 5 3581 126 60 20 26 12 86 977 0.0 5 709 117 69 43 23 16 87 912 0.0 5 698 118 44 24 18 10 88 858 0.0 5 650 94 62 29 14 9 89 743 0.0 5 548 94 44 22 16 19 90 683 0.0 5 496 92 40 24 14 17 91 725 0.0 5 515 107 51 27 18 7 92 614 0.0 5 431 92 48 22 12 9 93 612 0.0 5 451 64 42 30 16 9 94 509 0.0 5 365 62 30 20 22 10 95 507 0.0 5 361 67 29 18 15 17 96 435 0.0 5 288 55 38 27 13 14 97 392 0.0 5 283 46 27 17 12 7 98 356 0.0 5 241 44 30 16 13 12 99 346 0.0 5 239 36 30 26 12 3 100 301 0.0 5 218 37 21 7 14 4 101 271 0.0 5 180 34 23 17 12 5 102 243 0.0 5 168 32 14 13 10 6 103 225 0.0 5 164 22 12 8 8 11 104 196 0.0 5 145 18 14 7 4 8 105 155 0.0 5 117 16 9 5 2 6 106 126 0.0 5 88 15 11 5 2 5 107 120 0.0 5 86 11 8 5 3 7 108 102 0.0 5 72 5 7 9 4 5 109 82 0.0 5 57 7 7 5 3 3 110 77 0.0 5 58 4 4 4 4 3 111 81 0.0 5 70 2 2 5 1 1 112 49 0.0 5 39 1 2 3 3 1 113 50 0.0 5 41 2 2 0 2 3 114 48 0.0 5 40 2 1 2 2 1 115 178 0.0 5 170 4 2 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R1_val_1_val_1.fq.gz ============================================= 188375666 sequences processed in total