SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_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_7_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3396.86 s (23 µs/read; 2.63 M reads/minute). === Summary === Total reads processed: 149,080,064 Reads with adapters: 15,781,866 (10.6%) Reads written (passing filters): 149,080,064 (100.0%) Total basepairs processed: 14,336,134,965 bp Quality-trimmed: 2,861,987 bp (0.0%) Total written (filtered): 14,195,752,064 bp (99.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 15781866 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: 21.1% C: 5.3% G: 0.0% T: 73.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10148986 37270016.0 0 10148986 2 3024060 9317504.0 0 3024060 3 654853 2329376.0 0 654853 4 189120 582344.0 0 189120 5 57921 145586.0 0 57921 6 16863 36396.5 0 16863 7 7524 9099.1 0 7524 8 5391 2274.8 0 5391 9 5431 568.7 0 5431 10 9900 142.2 1 4991 4909 11 8910 35.5 1 4458 4452 12 7357 8.9 1 3843 3514 13 6758 2.2 1 3671 3087 14 5865 0.6 1 3204 2661 15 5223 0.1 1 2736 2487 16 4717 0.0 1 2565 2152 17 3787 0.0 1 2115 1672 18 3054 0.0 1 1982 1072 19 2871 0.0 1 1906 965 20 4159 0.0 2 1832 990 1337 21 3872 0.0 2 1829 882 1161 22 3590 0.0 2 1755 812 1023 23 3308 0.0 2 1616 812 880 24 3352 0.0 2 1685 800 867 25 2930 0.0 2 1474 733 723 26 2616 0.0 2 1318 662 636 27 2631 0.0 2 1400 632 599 28 2370 0.0 2 1282 598 490 29 2287 0.0 2 1279 563 445 30 2721 0.0 3 1116 555 413 637 31 2675 0.0 3 1191 558 391 535 32 2616 0.0 3 1140 521 391 564 33 2534 0.0 3 1144 498 359 533 34 2533 0.0 3 1094 548 407 484 35 2438 0.0 3 1076 541 369 452 36 2389 0.0 3 1094 483 387 425 37 2289 0.0 3 1111 515 316 347 38 2171 0.0 3 1054 487 341 289 39 2230 0.0 3 1077 529 321 303 40 2583 0.0 4 994 487 353 297 452 41 2463 0.0 4 961 467 323 279 433 42 2470 0.0 4 980 462 316 289 423 43 2405 0.0 4 931 485 316 295 378 44 2297 0.0 4 914 445 305 290 343 45 2255 0.0 4 911 410 332 257 345 46 2198 0.0 4 912 424 322 225 315 47 2255 0.0 4 956 454 304 248 293 48 2488 0.0 4 1107 516 366 298 201 49 4775 0.0 4 2066 1090 701 532 386 50 4939 0.0 5 1930 1053 703 528 400 325 51 3782 0.0 5 2046 691 424 268 216 137 52 3324 0.0 5 1907 610 337 209 147 114 53 3177 0.0 5 1950 553 292 169 126 87 54 2921 0.0 5 1840 515 227 157 105 77 55 2911 0.0 5 1888 476 250 148 91 58 56 2813 0.0 5 1963 423 181 109 66 71 57 2979 0.0 5 2156 379 210 107 76 51 58 3233 0.0 5 2459 383 178 102 60 51 59 3317 0.0 5 2597 359 159 94 59 49 60 2324 0.0 5 1666 325 164 79 59 31 61 2311 0.0 5 1700 302 140 89 50 30 62 2443 0.0 5 1858 292 159 57 49 28 63 2817 0.0 5 2297 296 106 70 25 23 64 3865 0.0 5 3312 301 113 66 47 26 65 2261 0.0 5 1716 288 139 61 43 14 66 2584 0.0 5 2062 268 127 62 44 21 67 2241 0.0 5 1741 275 111 53 39 22 68 2337 0.0 5 1876 263 104 55 26 13 69 2667 0.0 5 2220 268 90 41 25 23 70 4097 0.0 5 3648 251 99 43 35 21 71 8474 0.0 5 8011 264 102 44 26 27 72 50693 0.0 5 50202 292 108 36 34 21 73 94651 0.0 5 94131 310 111 52 27 20 74 827845 0.0 5 827358 304 94 49 27 13 75 39636 0.0 5 39209 257 83 45 25 17 76 30938 0.0 5 30538 228 79 40 29 24 77 172160 0.0 5 171816 205 59 33 25 22 78 15591 0.0 5 15248 201 67 37 25 13 79 104325 0.0 5 103986 172 91 39 19 18 80 23980 0.0 5 23662 172 70 34 27 15 81 13119 0.0 5 12812 157 69 39 21 21 82 34953 0.0 5 34688 139 49 37 22 18 83 6948 0.0 5 6693 131 60 28 21 15 84 27291 0.0 5 27015 143 59 41 17 16 85 6396 0.0 5 6161 127 50 27 18 13 86 1170 0.0 5 945 114 55 25 16 15 87 905 0.0 5 642 135 64 40 10 14 88 779 0.0 5 575 85 46 27 21 25 89 687 0.0 5 495 100 38 22 19 13 90 755 0.0 5 521 120 45 37 18 14 91 673 0.0 5 485 86 40 24 21 17 92 601 0.0 5 416 92 31 26 22 14 93 528 0.0 5 383 61 37 23 13 11 94 548 0.0 5 393 67 40 10 27 11 95 451 0.0 5 325 57 29 20 14 6 96 435 0.0 5 317 51 29 13 15 10 97 455 0.0 5 317 59 32 22 13 12 98 409 0.0 5 272 57 30 17 16 17 99 360 0.0 5 250 40 25 25 11 9 100 307 0.0 5 224 29 22 17 5 10 101 275 0.0 5 189 41 17 17 8 3 102 279 0.0 5 202 29 21 7 8 12 103 213 0.0 5 151 24 13 15 5 5 104 171 0.0 5 119 20 9 8 6 9 105 136 0.0 5 94 16 9 6 7 4 106 125 0.0 5 86 18 9 5 6 1 107 126 0.0 5 94 9 4 7 4 8 108 106 0.0 5 75 10 10 8 1 2 109 82 0.0 5 64 3 2 1 6 6 110 80 0.0 5 61 5 7 5 1 1 111 68 0.0 5 51 8 1 4 1 3 112 47 0.0 5 35 4 0 1 5 2 113 52 0.0 5 38 3 3 2 2 4 114 41 0.0 5 37 1 0 1 1 1 115 168 0.0 5 159 4 2 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R1_val_1_val_1.fq.gz ============================================= 149080064 sequences processed in total