SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2_val_2.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_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3468.66 s (23 µs/read; 2.58 M reads/minute). === Summary === Total reads processed: 149,080,064 Reads with adapters: 15,309,340 (10.3%) Reads written (passing filters): 149,080,064 (100.0%) Total basepairs processed: 14,333,353,408 bp Quality-trimmed: 3,668,034 bp (0.0%) Total written (filtered): 14,133,103,122 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 15309340 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: 14.2% C: 5.7% G: 0.0% T: 80.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9852792 37270016.0 0 9852792 2 2903952 9317504.0 0 2903952 3 633635 2329376.0 0 633635 4 181368 582344.0 0 181368 5 53687 145586.0 0 53687 6 13761 36396.5 0 13761 7 4483 9099.1 0 4483 8 2925 2274.8 0 2925 9 2551 568.7 0 2551 10 6976 142.2 1 2259 4717 11 5723 35.5 1 2131 3592 12 4665 8.9 1 1956 2709 13 4088 2.2 1 1740 2348 14 3606 0.6 1 1560 2046 15 3246 0.1 1 1413 1833 16 2789 0.0 1 1322 1467 17 2317 0.0 1 1085 1232 18 1825 0.0 1 1065 760 19 1673 0.0 1 961 712 20 3253 0.0 2 1274 682 1297 21 3157 0.0 2 1154 698 1305 22 2758 0.0 2 1031 603 1124 23 2841 0.0 2 1142 602 1097 24 2578 0.0 2 1060 533 985 25 2407 0.0 2 957 548 902 26 2300 0.0 2 914 537 849 27 1987 0.0 2 862 418 707 28 1674 0.0 2 840 394 440 29 1600 0.0 2 795 400 405 30 2432 0.0 3 806 377 423 826 31 2363 0.0 3 781 382 397 803 32 2345 0.0 3 821 339 383 802 33 2354 0.0 3 841 403 405 705 34 2174 0.0 3 798 331 374 671 35 1981 0.0 3 706 323 372 580 36 2007 0.0 3 778 346 330 553 37 1768 0.0 3 644 316 295 513 38 1662 0.0 3 677 345 285 355 39 1593 0.0 3 662 317 260 354 40 2257 0.0 4 703 328 266 323 637 41 2190 0.0 4 618 318 295 338 621 42 2159 0.0 4 728 322 230 291 588 43 2039 0.0 4 573 311 290 333 532 44 2072 0.0 4 666 310 285 299 512 45 1974 0.0 4 642 272 255 298 507 46 1900 0.0 4 717 289 231 245 418 47 1947 0.0 4 693 368 272 214 400 48 2295 0.0 4 817 487 363 319 309 49 4975 0.0 4 1646 1091 880 753 605 50 5255 0.0 5 1555 1086 801 713 598 502 51 3966 0.0 5 1564 803 555 424 350 270 52 3518 0.0 5 1548 715 461 338 243 213 53 3063 0.0 5 1391 601 402 305 209 155 54 2935 0.0 5 1502 566 314 232 171 150 55 2566 0.0 5 1355 465 286 192 158 110 56 2564 0.0 5 1426 443 286 164 140 105 57 2532 0.0 5 1483 454 233 159 109 94 58 2288 0.0 5 1337 386 215 157 112 81 59 2121 0.0 5 1280 354 209 122 80 76 60 1854 0.0 5 1136 308 155 114 82 59 61 1938 0.0 5 1218 315 169 89 90 57 62 1970 0.0 5 1305 303 154 91 80 37 63 1870 0.0 5 1247 292 132 91 63 45 64 1799 0.0 5 1213 285 121 81 69 30 65 1703 0.0 5 1184 237 109 81 49 43 66 1660 0.0 5 1153 261 122 53 44 27 67 1684 0.0 5 1245 209 108 66 35 21 68 1679 0.0 5 1251 199 122 51 26 30 69 1608 0.0 5 1199 201 87 58 43 20 70 1412 0.0 5 1029 178 86 54 41 24 71 1364 0.0 5 1024 174 68 45 30 23 72 1400 0.0 5 1095 145 71 34 25 30 73 1269 0.0 5 981 148 61 36 27 16 74 1303 0.0 5 987 160 75 48 18 15 75 1194 0.0 5 900 136 70 43 24 21 76 1226 0.0 5 979 123 53 37 21 13 77 1220 0.0 5 955 127 63 32 27 16 78 1030 0.0 5 806 104 36 36 26 22 79 997 0.0 5 787 109 47 24 20 10 80 982 0.0 5 793 85 43 23 24 14 81 973 0.0 5 774 97 39 20 24 19 82 934 0.0 5 747 92 42 25 14 14 83 854 0.0 5 666 93 37 24 15 19 84 828 0.0 5 664 96 25 21 13 9 85 865 0.0 5 694 91 40 15 15 10 86 828 0.0 5 664 82 37 23 12 10 87 748 0.0 5 610 64 25 18 19 12 88 781 0.0 5 625 68 46 11 20 11 89 672 0.0 5 528 67 30 22 16 9 90 659 0.0 5 525 60 28 22 13 11 91 602 0.0 5 453 59 39 28 15 8 92 575 0.0 5 435 62 31 21 12 14 93 572 0.0 5 451 47 27 12 24 11 94 549 0.0 5 434 53 23 21 7 11 95 521 0.0 5 422 44 22 8 11 14 96 488 0.0 5 383 44 28 15 11 7 97 514 0.0 5 415 43 21 12 13 10 98 424 0.0 5 335 29 12 21 15 12 99 495 0.0 5 393 39 19 23 11 10 100 444 0.0 5 366 35 16 10 10 7 101 428 0.0 5 339 42 21 11 2 13 102 433 0.0 5 331 38 29 16 11 8 103 382 0.0 5 305 30 12 16 10 9 104 365 0.0 5 291 28 17 14 6 9 105 400 0.0 5 317 32 19 12 15 5 106 357 0.0 5 272 36 15 18 11 5 107 391 0.0 5 309 29 21 9 11 12 108 359 0.0 5 279 33 9 19 10 9 109 411 0.0 5 332 25 22 15 7 10 110 520 0.0 5 416 42 17 20 11 14 111 606 0.0 5 472 48 28 17 33 8 112 887 0.0 5 750 43 31 21 23 19 113 1208 0.0 5 1034 64 41 24 28 17 114 3647 0.0 5 3348 110 65 45 37 42 115 1468546 0.0 5 1467891 325 148 75 61 46 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2_val_2.fq.gz ============================================= 149080064 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 149080064 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1561649 (1.05%)