SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_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_3_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4254.60 s (23 µs/read; 2.66 M reads/minute). === Summary === Total reads processed: 188,375,666 Reads with adapters: 21,144,092 (11.2%) Reads written (passing filters): 188,375,666 (100.0%) Total basepairs processed: 17,820,129,803 bp Quality-trimmed: 4,295,767 bp (0.0%) Total written (filtered): 17,363,855,972 bp (97.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21144092 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: 14.1% C: 5.6% G: 0.0% T: 80.4% none/other: 0.0% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 12434198 47093916.5 0 12434198 2 3725377 11773479.1 0 3725377 3 801023 2943369.8 0 801023 4 228671 735842.4 0 228671 5 68703 183960.6 0 68703 6 16655 45990.2 0 16655 7 5597 11497.5 0 5597 8 3566 2874.4 0 3566 9 3133 718.6 0 3133 10 8168 179.6 1 2810 5358 11 6672 44.9 1 2548 4124 12 5286 11.2 1 2312 2974 13 4543 2.8 1 2061 2482 14 4203 0.7 1 1847 2356 15 3670 0.2 1 1657 2013 16 3121 0.0 1 1466 1655 17 2758 0.0 1 1309 1449 18 2222 0.0 1 1290 932 19 1977 0.0 1 1121 856 20 3735 0.0 2 1540 796 1399 21 3562 0.0 2 1363 751 1448 22 3244 0.0 2 1362 680 1202 23 3257 0.0 2 1370 665 1222 24 3032 0.0 2 1296 666 1070 25 2929 0.0 2 1213 691 1025 26 2456 0.0 2 1075 561 820 27 2370 0.0 2 1083 538 749 28 2050 0.0 2 1091 469 490 29 1881 0.0 2 960 476 445 30 2815 0.0 3 949 426 486 954 31 2651 0.0 3 873 433 451 894 32 2637 0.0 3 902 460 432 843 33 2545 0.0 3 932 412 390 811 34 2538 0.0 3 914 426 422 776 35 2261 0.0 3 765 433 381 682 36 2259 0.0 3 902 370 393 594 37 2016 0.0 3 826 371 300 519 38 1944 0.0 3 860 391 321 372 39 1790 0.0 3 721 385 308 376 40 2669 0.0 4 866 393 340 357 713 41 2476 0.0 4 748 353 341 385 649 42 2489 0.0 4 808 341 343 368 629 43 2390 0.0 4 652 370 340 379 649 44 2341 0.0 4 742 378 305 326 590 45 2277 0.0 4 789 337 311 322 518 46 2242 0.0 4 836 379 269 294 464 47 2189 0.0 4 858 412 248 251 420 48 2677 0.0 4 1016 532 411 364 354 49 5724 0.0 4 1966 1306 981 797 674 50 5877 0.0 5 1794 1218 942 745 626 552 51 4634 0.0 5 1897 886 668 487 375 321 52 4049 0.0 5 1856 798 508 379 294 214 53 3661 0.0 5 1783 654 471 322 258 173 54 3510 0.0 5 1793 689 429 250 209 140 55 3232 0.0 5 1770 573 341 224 193 131 56 3073 0.0 5 1728 549 317 168 177 134 57 2966 0.0 5 1796 504 288 154 121 103 58 2925 0.0 5 1809 485 263 152 129 87 59 2455 0.0 5 1494 405 229 133 109 85 60 2349 0.0 5 1457 364 215 142 102 69 61 2415 0.0 5 1515 421 209 115 94 61 62 2338 0.0 5 1544 351 186 120 71 66 63 2278 0.0 5 1547 339 173 91 69 59 64 2302 0.0 5 1565 339 164 100 80 54 65 2150 0.0 5 1518 289 146 83 73 41 66 2107 0.0 5 1481 300 135 89 55 47 67 2135 0.0 5 1554 278 119 75 59 50 68 2183 0.0 5 1665 246 96 90 46 40 69 2150 0.0 5 1590 281 126 59 49 45 70 1914 0.0 5 1402 259 113 72 47 21 71 1747 0.0 5 1321 205 96 62 36 27 72 1822 0.0 5 1378 226 84 52 54 28 73 1675 0.0 5 1281 205 78 50 37 24 74 1587 0.0 5 1216 183 90 40 38 20 75 1582 0.0 5 1263 152 71 47 32 17 76 1592 0.0 5 1259 154 75 42 38 24 77 1563 0.0 5 1273 135 69 40 26 20 78 1366 0.0 5 1070 152 52 50 25 17 79 1251 0.0 5 1004 125 57 32 15 18 80 1382 0.0 5 1113 149 41 38 25 16 81 1266 0.0 5 1028 119 58 27 17 17 82 1153 0.0 5 931 110 47 26 21 18 83 1100 0.0 5 905 105 46 16 20 8 84 1055 0.0 5 860 83 41 36 20 15 85 1161 0.0 5 950 103 49 28 19 12 86 1030 0.0 5 831 103 44 21 18 13 87 991 0.0 5 798 85 37 30 26 15 88 959 0.0 5 772 80 48 24 22 13 89 905 0.0 5 727 84 37 25 13 19 90 876 0.0 5 689 88 55 19 14 11 91 783 0.0 5 615 81 31 21 18 17 92 862 0.0 5 697 74 41 24 16 10 93 787 0.0 5 624 65 41 18 20 19 94 743 0.0 5 597 72 25 23 17 9 95 724 0.0 5 592 58 31 15 13 15 96 726 0.0 5 598 64 25 19 9 11 97 690 0.0 5 580 48 31 10 10 11 98 633 0.0 5 503 55 35 13 16 11 99 598 0.0 5 472 55 32 15 10 14 100 570 0.0 5 458 48 18 19 17 10 101 548 0.0 5 441 50 21 16 11 9 102 583 0.0 5 463 49 27 26 8 10 103 510 0.0 5 415 39 21 14 8 13 104 477 0.0 5 387 29 20 16 13 12 105 514 0.0 5 428 31 21 13 10 11 106 480 0.0 5 392 32 14 19 8 15 107 488 0.0 5 384 36 26 17 13 12 108 441 0.0 5 346 39 19 14 8 15 109 575 0.0 5 461 35 23 18 19 19 110 735 0.0 5 601 41 27 20 21 25 111 731 0.0 5 605 48 26 21 13 18 112 1160 0.0 5 984 51 31 35 30 29 113 1555 0.0 5 1312 88 47 43 26 39 114 4928 0.0 5 4567 157 89 43 39 33 115 3627496 0.0 5 3626617 451 198 98 81 51 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R2_val_2_val_2.fq.gz ============================================= 188375666 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 188375666 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3749793 (1.99%)