SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_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_1_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3900.62 s (24 µs/read; 2.48 M reads/minute). === Summary === Total reads processed: 161,104,708 Reads with adapters: 17,875,932 (11.1%) Reads written (passing filters): 161,104,708 (100.0%) Total basepairs processed: 16,001,858,566 bp Quality-trimmed: 3,273,494 bp (0.0%) Total written (filtered): 15,778,099,632 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17875932 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: 24.7% C: 4.8% G: 0.0% T: 70.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10884348 40276177.0 0 10884348 2 3228008 10069044.2 0 3228008 3 699678 2517261.1 0 699678 4 201565 629315.3 0 201565 5 59981 157328.8 0 59981 6 17764 39332.2 0 17764 7 7890 9833.1 0 7890 8 5644 2458.3 0 5644 9 5575 614.6 0 5575 10 10369 153.6 1 5164 5205 11 9180 38.4 1 4650 4530 12 7582 9.6 1 4084 3498 13 6734 2.4 1 3626 3108 14 6106 0.6 1 3225 2881 15 5445 0.2 1 2998 2447 16 4828 0.0 1 2657 2171 17 3902 0.0 1 2218 1684 18 3293 0.0 1 2161 1132 19 3037 0.0 1 1996 1041 20 4549 0.0 2 2075 1029 1445 21 3975 0.0 2 1867 934 1174 22 3721 0.0 2 1824 874 1023 23 3568 0.0 2 1824 814 930 24 3385 0.0 2 1719 798 868 25 3082 0.0 2 1567 740 775 26 2909 0.0 2 1476 689 744 27 2779 0.0 2 1430 672 677 28 2467 0.0 2 1429 612 426 29 2296 0.0 2 1275 577 444 30 2887 0.0 3 1247 593 398 649 31 2829 0.0 3 1262 549 443 575 32 2694 0.0 3 1156 533 424 581 33 2602 0.0 3 1141 557 378 526 34 2661 0.0 3 1172 551 402 536 35 2562 0.0 3 1105 571 404 482 36 2512 0.0 3 1134 529 391 458 37 2287 0.0 3 1074 488 306 419 38 2236 0.0 3 1105 481 347 303 39 2145 0.0 3 1107 467 299 272 40 2597 0.0 4 1034 468 337 281 477 41 2508 0.0 4 1014 466 296 277 455 42 2489 0.0 4 980 480 299 289 441 43 2576 0.0 4 1009 505 353 312 397 44 2240 0.0 4 881 449 287 272 351 45 2247 0.0 4 891 428 305 266 357 46 2227 0.0 4 954 448 255 229 341 47 2241 0.0 4 979 449 297 237 279 48 2571 0.0 4 1192 560 360 237 222 49 4774 0.0 4 2065 1061 717 526 405 50 5067 0.0 5 2042 1083 692 491 413 346 51 3718 0.0 5 1932 700 437 294 190 165 52 3387 0.0 5 1884 637 361 232 156 117 53 3143 0.0 5 1872 541 301 200 129 100 54 3120 0.0 5 1950 518 274 161 123 94 55 2889 0.0 5 1892 474 254 125 86 58 56 2872 0.0 5 1933 438 231 132 98 40 57 3108 0.0 5 2256 414 203 113 68 54 58 3847 0.0 5 3034 408 198 102 60 45 59 3848 0.0 5 3123 391 174 73 57 30 60 2354 0.0 5 1683 353 145 81 47 45 61 2370 0.0 5 1803 306 127 77 40 17 62 2655 0.0 5 2052 318 148 73 36 28 63 3468 0.0 5 2908 277 140 74 47 22 64 5285 0.0 5 4725 299 134 59 44 24 65 2617 0.0 5 1988 307 186 74 37 25 66 3197 0.0 5 2612 316 142 69 38 20 67 2602 0.0 5 2108 269 106 62 38 19 68 2800 0.0 5 2300 287 102 49 40 22 69 3628 0.0 5 3094 290 118 62 37 27 70 7032 0.0 5 6545 303 91 50 29 14 71 16115 0.0 5 15578 332 100 55 32 18 72 104862 0.0 5 104244 402 107 68 26 15 73 183893 0.0 5 183291 398 106 45 32 21 74 1469317 0.0 5 1468746 372 99 48 36 16 75 48741 0.0 5 48314 250 96 42 28 11 76 46631 0.0 5 46236 224 79 44 30 18 77 287320 0.0 5 286940 209 73 55 25 18 78 22515 0.0 5 22193 185 67 28 19 23 79 184264 0.0 5 183942 157 72 48 24 21 80 44340 0.0 5 44052 155 63 30 20 20 81 22849 0.0 5 22564 142 58 42 21 22 82 67259 0.0 5 67016 118 57 35 21 12 83 6009 0.0 5 5730 129 71 43 18 18 84 28039 0.0 5 27769 141 55 38 23 13 85 5635 0.0 5 5415 124 46 27 14 9 86 834 0.0 5 633 100 43 28 14 16 87 733 0.0 5 525 114 39 25 19 11 88 723 0.0 5 538 87 48 21 15 14 89 604 0.0 5 436 81 42 20 16 9 90 660 0.0 5 452 91 46 35 21 15 91 602 0.0 5 427 77 36 33 18 11 92 523 0.0 5 365 75 38 20 16 9 93 491 0.0 5 343 65 39 25 11 8 94 482 0.0 5 328 79 31 25 10 9 95 451 0.0 5 317 57 32 21 11 13 96 383 0.0 5 259 60 20 26 11 7 97 388 0.0 5 260 66 24 16 14 8 98 338 0.0 5 253 49 9 14 9 4 99 313 0.0 5 231 28 21 13 14 6 100 287 0.0 5 186 39 22 21 12 7 101 270 0.0 5 189 40 16 4 13 8 102 222 0.0 5 155 19 16 11 7 14 103 186 0.0 5 127 24 11 5 11 8 104 177 0.0 5 126 16 10 11 8 6 105 130 0.0 5 90 10 15 9 5 1 106 130 0.0 5 88 15 6 10 4 7 107 92 0.0 5 65 6 8 8 2 3 108 78 0.0 5 60 9 2 1 3 3 109 78 0.0 5 58 4 8 3 3 2 110 78 0.0 5 59 4 4 2 6 3 111 68 0.0 5 52 6 0 3 5 2 112 46 0.0 5 33 3 3 2 2 3 113 34 0.0 5 23 4 3 2 1 1 114 52 0.0 5 39 6 4 1 1 1 115 138 0.0 5 125 5 4 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R1_val_1_val_1.fq.gz ============================================= 161104708 sequences processed in total