SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_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_2_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4017.41 s (24 µs/read; 2.49 M reads/minute). === Summary === Total reads processed: 166,832,019 Reads with adapters: 17,423,292 (10.4%) Reads written (passing filters): 166,832,019 (100.0%) Total basepairs processed: 16,548,960,510 bp Quality-trimmed: 4,272,473 bp (0.0%) Total written (filtered): 16,284,859,854 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17423292 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: 14.0% C: 5.4% G: 0.0% T: 80.6% none/other: 0.1% 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 11020761 41708004.8 0 11020761 2 3225765 10427001.2 0 3225765 3 700743 2606750.3 0 700743 4 199754 651687.6 0 199754 5 58835 162921.9 0 58835 6 14425 40730.5 0 14425 7 4917 10182.6 0 4917 8 2830 2545.7 0 2830 9 2613 636.4 0 2613 10 7299 159.1 1 2320 4979 11 6085 39.8 1 2148 3937 12 4966 9.9 1 2064 2902 13 4195 2.5 1 1746 2449 14 3940 0.6 1 1633 2307 15 3285 0.2 1 1471 1814 16 2784 0.0 1 1245 1539 17 2348 0.0 1 1094 1254 18 1916 0.0 1 1077 839 19 1798 0.0 1 995 803 20 3512 0.0 2 1289 726 1497 21 3212 0.0 2 1169 700 1343 22 3100 0.0 2 1115 695 1290 23 2982 0.0 2 1132 632 1218 24 2669 0.0 2 981 624 1064 25 2628 0.0 2 992 607 1029 26 2252 0.0 2 885 481 886 27 1964 0.0 2 854 409 701 28 1764 0.0 2 858 411 495 29 1682 0.0 2 804 413 465 30 2621 0.0 3 791 365 517 948 31 2450 0.0 3 708 384 426 932 32 2336 0.0 3 738 371 406 821 33 2274 0.0 3 725 375 397 777 34 2321 0.0 3 746 395 381 799 35 2150 0.0 3 678 385 388 699 36 1879 0.0 3 684 292 337 566 37 1783 0.0 3 631 322 294 536 38 1574 0.0 3 600 330 281 363 39 1542 0.0 3 564 318 281 379 40 2247 0.0 4 597 292 296 358 704 41 2171 0.0 4 524 341 275 329 702 42 2112 0.0 4 581 294 271 344 622 43 1987 0.0 4 495 284 267 346 595 44 2064 0.0 4 608 293 261 327 575 45 1972 0.0 4 610 241 252 317 552 46 1916 0.0 4 633 280 218 301 484 47 1874 0.0 4 635 331 279 229 400 48 2176 0.0 4 725 442 387 346 276 49 5033 0.0 4 1567 1109 872 823 662 50 5243 0.0 5 1414 1081 876 689 636 547 51 4068 0.0 5 1510 823 613 457 360 305 52 3448 0.0 5 1453 687 474 361 249 224 53 3045 0.0 5 1337 643 366 269 240 190 54 2912 0.0 5 1350 580 370 264 193 155 55 2651 0.0 5 1304 516 296 213 209 113 56 2488 0.0 5 1295 447 285 207 143 111 57 2257 0.0 5 1267 403 231 175 113 68 58 2249 0.0 5 1288 397 227 150 98 89 59 1962 0.0 5 1091 347 200 138 109 77 60 1844 0.0 5 1112 288 188 122 74 60 61 1802 0.0 5 1106 295 163 103 85 50 62 1731 0.0 5 1070 303 157 101 62 38 63 1680 0.0 5 1076 261 144 88 62 49 64 1678 0.0 5 1076 263 136 90 65 48 65 1661 0.0 5 1093 250 133 95 48 42 66 1503 0.0 5 1025 234 112 58 47 27 67 1650 0.0 5 1148 225 120 77 46 34 68 1664 0.0 5 1215 222 114 43 48 22 69 1460 0.0 5 1087 186 79 49 32 27 70 1305 0.0 5 952 190 72 38 26 27 71 1266 0.0 5 943 151 81 50 25 16 72 1259 0.0 5 926 159 78 48 30 18 73 1158 0.0 5 852 157 57 42 29 21 74 1088 0.0 5 823 120 55 40 22 28 75 1072 0.0 5 815 123 65 39 15 15 76 1108 0.0 5 868 113 62 31 19 15 77 1066 0.0 5 817 124 56 34 16 19 78 893 0.0 5 704 87 52 21 16 13 79 883 0.0 5 680 99 48 28 19 9 80 919 0.0 5 729 94 33 31 18 14 81 788 0.0 5 638 80 31 16 14 9 82 731 0.0 5 583 60 31 26 13 18 83 795 0.0 5 626 82 30 22 16 19 84 685 0.0 5 526 69 41 18 19 12 85 756 0.0 5 597 61 41 26 19 12 86 656 0.0 5 517 65 30 23 10 11 87 647 0.0 5 509 65 26 19 14 14 88 701 0.0 5 561 63 24 16 21 16 89 605 0.0 5 468 60 34 19 15 9 90 580 0.0 5 432 77 24 19 17 11 91 536 0.0 5 431 44 26 17 10 8 92 515 0.0 5 407 48 27 13 11 9 93 522 0.0 5 408 63 23 11 9 8 94 540 0.0 5 430 51 21 15 11 12 95 494 0.0 5 393 42 23 21 6 9 96 419 0.0 5 337 31 13 15 9 14 97 497 0.0 5 394 45 24 16 7 11 98 418 0.0 5 324 38 22 14 17 3 99 421 0.0 5 327 48 12 14 11 9 100 384 0.0 5 294 26 23 17 13 11 101 399 0.0 5 320 37 10 9 12 11 102 381 0.0 5 304 20 26 12 11 8 103 387 0.0 5 311 31 15 9 6 15 104 339 0.0 5 275 18 19 13 7 7 105 394 0.0 5 326 31 6 12 11 8 106 410 0.0 5 327 32 12 16 11 12 107 400 0.0 5 315 26 13 17 15 14 108 360 0.0 5 278 29 13 11 17 12 109 456 0.0 5 367 32 14 17 13 13 110 549 0.0 5 460 22 19 16 19 13 111 580 0.0 5 463 38 26 23 12 18 112 921 0.0 5 750 49 33 30 29 30 113 1304 0.0 5 1108 62 43 24 33 34 114 3982 0.0 5 3628 140 67 61 46 40 115 2002221 0.0 5 2001464 342 181 103 81 50 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_2_R2_val_2_val_2.fq.gz ============================================= 166832019 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 166832019 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2094853 (1.26%)