SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_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_2_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3936.08 s (24 µs/read; 2.54 M reads/minute). === Summary === Total reads processed: 166,832,019 Reads with adapters: 17,883,352 (10.7%) Reads written (passing filters): 166,832,019 (100.0%) Total basepairs processed: 16,549,204,997 bp Quality-trimmed: 3,301,519 bp (0.0%) Total written (filtered): 16,366,200,743 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17883352 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: 21.8% C: 5.0% G: 0.0% T: 73.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11285978 41708004.8 0 11285978 2 3352840 10427001.2 0 3352840 3 722486 2606750.3 0 722486 4 206221 651687.6 0 206221 5 62359 162921.9 0 62359 6 17727 40730.5 0 17727 7 8073 10182.6 0 8073 8 5535 2545.7 0 5535 9 5745 636.4 0 5745 10 10634 159.1 1 5435 5199 11 9278 39.8 1 4850 4428 12 7801 9.9 1 4112 3689 13 6950 2.5 1 3672 3278 14 6400 0.6 1 3483 2917 15 5472 0.2 1 2978 2494 16 5001 0.0 1 2745 2256 17 3825 0.0 1 2162 1663 18 3311 0.0 1 2114 1197 19 3120 0.0 1 2073 1047 20 4630 0.0 2 2149 1006 1475 21 4080 0.0 2 1986 944 1150 22 3745 0.0 2 1863 823 1059 23 3551 0.0 2 1760 858 933 24 3579 0.0 2 1805 861 913 25 3174 0.0 2 1619 746 809 26 2994 0.0 2 1487 784 723 27 2874 0.0 2 1563 668 643 28 2729 0.0 2 1489 719 521 29 2423 0.0 2 1390 605 428 30 3066 0.0 3 1361 613 461 631 31 2886 0.0 3 1292 583 421 590 32 2869 0.0 3 1259 581 437 592 33 2719 0.0 3 1237 524 417 541 34 2706 0.0 3 1142 584 438 542 35 2620 0.0 3 1137 581 401 501 36 2605 0.0 3 1167 572 381 485 37 2527 0.0 3 1219 549 341 418 38 2360 0.0 3 1196 571 320 273 39 2267 0.0 3 1111 513 324 319 40 2617 0.0 4 1055 515 358 280 409 41 2581 0.0 4 1015 479 341 283 463 42 2537 0.0 4 1031 469 340 303 394 43 2455 0.0 4 949 483 340 307 376 44 2345 0.0 4 985 456 287 271 346 45 2326 0.0 4 967 439 314 265 341 46 2157 0.0 4 900 434 279 263 281 47 2314 0.0 4 1030 522 284 206 272 48 2529 0.0 4 1149 551 357 244 228 49 4582 0.0 4 1920 1047 685 547 383 50 4836 0.0 5 2029 1052 649 474 342 290 51 3641 0.0 5 1968 657 419 270 174 153 52 3165 0.0 5 1834 561 321 205 135 109 53 3091 0.0 5 1887 559 288 167 97 93 54 3064 0.0 5 1981 492 267 144 118 62 55 2875 0.0 5 1880 459 251 157 73 55 56 2987 0.0 5 2110 414 202 118 89 54 57 3463 0.0 5 2601 428 196 117 70 51 58 3356 0.0 5 2633 359 165 99 51 49 59 2894 0.0 5 2236 326 160 84 47 41 60 2354 0.0 5 1688 328 157 92 57 32 61 2416 0.0 5 1834 319 118 76 43 26 62 2930 0.0 5 2353 283 154 71 45 24 63 3818 0.0 5 3204 341 134 62 43 34 64 3488 0.0 5 2953 291 109 81 20 34 65 2414 0.0 5 1820 297 154 88 36 19 66 2758 0.0 5 2172 315 143 61 41 26 67 2491 0.0 5 1931 305 137 56 44 18 68 2778 0.0 5 2293 264 116 48 34 23 69 3854 0.0 5 3347 309 93 49 28 28 70 8046 0.0 5 7522 325 99 54 20 26 71 24602 0.0 5 24038 354 102 48 38 22 72 80938 0.0 5 80393 328 95 56 38 28 73 316767 0.0 5 316233 315 115 48 33 23 74 953499 0.0 5 952998 295 98 53 38 17 75 43254 0.0 5 42782 266 92 58 29 27 76 77338 0.0 5 76893 241 94 55 29 26 77 179877 0.0 5 179490 207 84 54 26 16 78 43978 0.0 5 43586 219 93 37 26 17 79 115275 0.0 5 114886 199 84 56 32 18 80 30555 0.0 5 30229 158 84 38 22 24 81 26012 0.0 5 25637 198 94 32 28 23 82 37525 0.0 5 37254 144 58 27 31 11 83 18735 0.0 5 18440 151 64 34 21 25 84 32421 0.0 5 32135 140 71 36 24 15 85 5987 0.0 5 5719 124 61 39 25 19 86 1179 0.0 5 946 116 48 30 24 15 87 818 0.0 5 583 108 50 35 28 14 88 715 0.0 5 493 106 56 23 14 23 89 690 0.0 5 500 86 43 19 25 17 90 680 0.0 5 472 87 54 28 22 17 91 637 0.0 5 450 92 46 24 13 12 92 570 0.0 5 376 82 46 32 20 14 93 521 0.0 5 375 59 43 17 19 8 94 475 0.0 5 320 74 43 14 10 14 95 411 0.0 5 271 51 36 24 15 14 96 459 0.0 5 300 65 36 22 20 16 97 379 0.0 5 253 54 23 27 12 10 98 328 0.0 5 223 50 24 10 15 6 99 305 0.0 5 210 44 26 10 9 6 100 308 0.0 5 199 41 27 17 15 9 101 303 0.0 5 210 29 22 18 16 8 102 227 0.0 5 158 20 22 12 12 3 103 198 0.0 5 146 17 11 8 7 9 104 155 0.0 5 113 13 10 11 4 4 105 139 0.0 5 101 14 9 11 1 3 106 105 0.0 5 70 10 7 8 6 4 107 100 0.0 5 72 9 6 5 2 6 108 94 0.0 5 65 8 4 3 8 6 109 70 0.0 5 53 6 3 1 2 5 110 70 0.0 5 55 3 2 5 0 5 111 62 0.0 5 50 3 2 2 1 4 112 43 0.0 5 28 2 4 4 1 4 113 31 0.0 5 22 2 0 2 2 3 114 35 0.0 5 28 2 3 2 115 160 0.0 5 144 5 5 2 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R1_val_1_val_1.fq.gz ============================================= 166832019 sequences processed in total