SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_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_8_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3629.43 s (22 µs/read; 2.67 M reads/minute). === Summary === Total reads processed: 161,309,784 Reads with adapters: 17,262,120 (10.7%) Reads written (passing filters): 161,309,784 (100.0%) Total basepairs processed: 15,578,048,811 bp Quality-trimmed: 3,003,729 bp (0.0%) Total written (filtered): 15,408,768,753 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17262120 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: 21.5% C: 5.0% G: 0.0% T: 73.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10929782 40327446.0 0 10929782 2 3286493 10081861.5 0 3286493 3 707881 2520465.4 0 707881 4 202931 630116.3 0 202931 5 60454 157529.1 0 60454 6 17546 39382.3 0 17546 7 7906 9845.6 0 7906 8 5715 2461.4 0 5715 9 5467 615.3 0 5467 10 10075 153.8 1 5095 4980 11 8735 38.5 1 4527 4208 12 7645 9.6 1 4103 3542 13 6792 2.4 1 3687 3105 14 6118 0.6 1 3335 2783 15 5278 0.2 1 2828 2450 16 4548 0.0 1 2549 1999 17 3790 0.0 1 2120 1670 18 3078 0.0 1 2013 1065 19 2834 0.0 1 1887 947 20 4180 0.0 2 1939 928 1313 21 3850 0.0 2 1856 883 1111 22 3403 0.0 2 1717 736 950 23 3238 0.0 2 1591 806 841 24 3337 0.0 2 1678 815 844 25 3053 0.0 2 1567 746 740 26 2630 0.0 2 1329 663 638 27 2556 0.0 2 1388 605 563 28 2403 0.0 2 1349 594 460 29 2235 0.0 2 1284 544 407 30 2766 0.0 3 1244 578 367 577 31 2596 0.0 3 1116 508 429 543 32 2566 0.0 3 1094 521 419 532 33 2525 0.0 3 1127 540 384 474 34 2425 0.0 3 1073 517 363 472 35 2390 0.0 3 1044 509 374 463 36 2361 0.0 3 1063 508 358 432 37 2240 0.0 3 1037 484 325 394 38 1955 0.0 3 966 467 282 240 39 1963 0.0 3 916 498 309 240 40 2293 0.0 4 909 438 298 263 385 41 2412 0.0 4 948 453 317 294 400 42 2434 0.0 4 1018 462 315 253 386 43 2346 0.0 4 926 488 307 256 369 44 2329 0.0 4 920 467 317 246 379 45 2065 0.0 4 876 379 225 237 348 46 2211 0.0 4 939 453 258 248 313 47 2164 0.0 4 991 462 274 185 252 48 2469 0.0 4 1072 531 367 279 220 49 4643 0.0 4 2035 1048 686 485 389 50 4889 0.0 5 2003 1010 673 488 396 319 51 3690 0.0 5 2022 669 410 250 185 154 52 3186 0.0 5 1807 577 297 212 174 119 53 2985 0.0 5 1855 505 271 174 110 70 54 2880 0.0 5 1818 481 257 165 93 66 55 2764 0.0 5 1794 452 248 130 81 59 56 2846 0.0 5 1965 419 203 129 78 52 57 3086 0.0 5 2290 371 209 105 68 43 58 3402 0.0 5 2635 371 187 96 68 45 59 3310 0.0 5 2692 306 135 79 69 29 60 2305 0.0 5 1692 317 135 82 43 36 61 2211 0.0 5 1688 268 128 62 41 24 62 2621 0.0 5 2105 285 107 64 28 32 63 3277 0.0 5 2820 227 115 58 31 26 64 3821 0.0 5 3285 299 112 56 41 28 65 2292 0.0 5 1792 244 135 76 23 22 66 2589 0.0 5 2133 259 97 54 31 15 67 2294 0.0 5 1844 263 94 43 34 16 68 2461 0.0 5 2018 260 83 56 30 14 69 3201 0.0 5 2722 280 103 54 27 15 70 5481 0.0 5 5053 240 85 49 34 20 71 14421 0.0 5 13979 276 77 51 26 12 72 63317 0.0 5 62847 308 87 43 23 9 73 204838 0.0 5 204340 326 78 44 33 17 74 969623 0.0 5 969148 290 83 51 31 20 75 47299 0.0 5 46893 238 75 46 33 14 76 57319 0.0 5 56971 211 56 44 21 16 77 202036 0.0 5 201682 218 67 34 24 11 78 29232 0.0 5 28911 167 67 40 28 19 79 120785 0.0 5 120501 150 67 31 13 23 80 29689 0.0 5 29402 159 65 27 24 12 81 20327 0.0 5 20043 148 62 33 23 18 82 36983 0.0 5 36742 109 56 40 27 9 83 9014 0.0 5 8787 115 53 29 15 15 84 15364 0.0 5 15135 130 54 18 13 14 85 3288 0.0 5 3093 108 50 18 13 6 86 823 0.0 5 641 92 41 26 11 12 87 793 0.0 5 605 103 33 27 13 12 88 720 0.0 5 551 94 42 14 12 7 89 653 0.0 5 497 78 32 22 8 16 90 655 0.0 5 516 79 33 13 8 6 91 635 0.0 5 451 86 45 25 20 8 92 569 0.0 5 432 62 39 17 14 5 93 539 0.0 5 384 75 33 21 16 10 94 468 0.0 5 333 59 30 19 17 10 95 438 0.0 5 319 55 25 21 15 3 96 400 0.0 5 289 50 31 6 13 11 97 403 0.0 5 288 52 25 13 14 11 98 345 0.0 5 246 44 26 11 9 9 99 322 0.0 5 242 31 18 12 9 10 100 280 0.0 5 196 28 24 13 14 5 101 251 0.0 5 185 18 19 10 9 10 102 225 0.0 5 172 24 12 4 6 7 103 183 0.0 5 147 15 6 8 5 2 104 176 0.0 5 118 30 10 10 3 5 105 163 0.0 5 108 22 12 8 6 7 106 119 0.0 5 91 16 4 2 3 3 107 101 0.0 5 75 3 5 11 3 4 108 92 0.0 5 68 6 4 3 4 7 109 84 0.0 5 61 5 5 2 7 4 110 77 0.0 5 56 3 5 4 6 3 111 64 0.0 5 42 6 5 4 4 3 112 53 0.0 5 39 7 1 2 1 3 113 40 0.0 5 30 5 1 1 2 1 114 46 0.0 5 42 2 0 1 1 115 171 0.0 5 164 2 2 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R1_val_1_val_1.fq.gz ============================================= 161309784 sequences processed in total