SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 105.81 s (26 us/read; 2.27 M reads/minute). === Summary === Total reads processed: 3,996,315 Reads with adapters: 2,414,527 (60.4%) Reads written (passing filters): 3,996,315 (100.0%) Total basepairs processed: 593,062,263 bp Quality-trimmed: 140,474 bp (0.0%) Total written (filtered): 563,799,510 bp (95.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2414527 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 27.6% G: 20.3% T: 20.3% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 1131131 999078.8 0 1131131 2 218514 249769.7 0 218514 3 92634 62442.4 0 92634 4 69282 15610.6 0 69282 5 947 3902.7 0 947 6 26669 975.7 0 26669 7 23335 243.9 0 23335 8 27529 61.0 0 27529 9 24387 15.2 0 24268 119 10 25314 3.8 1 23754 1560 11 26283 1.0 1 23938 2345 12 49032 0.2 1 45917 3115 13 1383 0.1 1 889 494 14 48217 0.1 1 44794 3423 15 1073 0.1 1 659 414 16 50306 0.1 1 46248 4058 17 1566 0.1 1 1024 542 18 30527 0.1 1 28070 2457 19 76707 0.1 1 72330 4377 20 483 0.1 1 293 190 21 170 0.1 1 116 54 22 411 0.1 1 266 145 23 23809 0.1 1 22004 1805 24 56486 0.1 1 52715 3771 25 1264 0.1 1 847 417 26 20025 0.1 1 18597 1428 27 17927 0.1 1 16880 1047 28 351 0.1 1 223 128 29 17811 0.1 1 16451 1360 30 21046 0.1 1 19611 1435 31 27126 0.1 1 25585 1541 32 916 0.1 1 652 264 33 29781 0.1 1 27735 2046 34 397 0.1 1 263 134 35 13349 0.1 1 12548 801 36 13531 0.1 1 12645 886 37 14307 0.1 1 13290 1017 38 22347 0.1 1 20934 1413 39 332 0.1 1 246 86 40 11397 0.1 1 10684 713 41 9994 0.1 1 9415 579 42 12897 0.1 1 12021 876 43 9858 0.1 1 8895 963 44 23703 0.1 1 22141 1562 45 4875 0.1 1 4557 318 46 4502 0.1 1 4081 421 47 589 0.1 1 397 192 48 31741 0.1 1 30092 1649 49 16981 0.1 1 16147 834 50 2554 0.1 1 2298 256 51 7633 0.1 1 7163 470 52 7621 0.1 1 7210 411 53 1435 0.1 1 1306 129 54 296 0.1 1 239 57 55 4039 0.1 1 3828 211 56 2670 0.1 1 2494 176 57 335 0.1 1 292 43 58 887 0.1 1 818 69 59 1073 0.1 1 980 93 60 420 0.1 1 369 51 61 755 0.1 1 685 70 62 2440 0.1 1 2318 122 63 473 0.1 1 428 45 64 769 0.1 1 725 44 65 690 0.1 1 625 65 66 2129 0.1 1 2034 95 67 407 0.1 1 365 42 68 567 0.1 1 529 38 69 620 0.1 1 561 59 70 613 0.1 1 564 49 71 236 0.1 1 214 22 72 340 0.1 1 305 35 73 568 0.1 1 529 39 74 809 0.1 1 763 46 75 909 0.1 1 847 62 76 869 0.1 1 818 51 77 850 0.1 1 806 44 78 779 0.1 1 728 51 79 785 0.1 1 753 32 80 767 0.1 1 722 45 81 665 0.1 1 622 43 82 614 0.1 1 569 45 83 595 0.1 1 557 38 84 523 0.1 1 491 32 85 468 0.1 1 441 27 86 442 0.1 1 408 34 87 418 0.1 1 376 42 88 418 0.1 1 393 25 89 362 0.1 1 339 23 90 368 0.1 1 341 27 91 365 0.1 1 321 44 92 279 0.1 1 261 18 93 253 0.1 1 238 15 94 279 0.1 1 262 17 95 199 0.1 1 180 19 96 252 0.1 1 226 26 97 220 0.1 1 204 16 98 201 0.1 1 191 10 99 180 0.1 1 163 17 100 173 0.1 1 158 15 101 153 0.1 1 143 10 102 113 0.1 1 105 8 103 147 0.1 1 131 16 104 129 0.1 1 114 15 105 101 0.1 1 95 6 106 102 0.1 1 92 10 107 98 0.1 1 85 13 108 70 0.1 1 62 8 109 95 0.1 1 86 9 110 76 0.1 1 63 13 111 84 0.1 1 77 7 112 76 0.1 1 69 7 113 89 0.1 1 82 7 114 51 0.1 1 43 8 115 79 0.1 1 67 12 116 56 0.1 1 52 4 117 50 0.1 1 45 5 118 70 0.1 1 64 6 119 55 0.1 1 49 6 120 74 0.1 1 66 8 121 52 0.1 1 41 11 122 71 0.1 1 69 2 123 47 0.1 1 42 5 124 67 0.1 1 63 4 125 73 0.1 1 71 2 126 91 0.1 1 86 5 127 66 0.1 1 62 4 128 106 0.1 1 100 6 129 102 0.1 1 100 2 130 70 0.1 1 64 6 131 90 0.1 1 84 6 132 90 0.1 1 84 6 133 85 0.1 1 83 2 134 91 0.1 1 86 5 135 99 0.1 1 91 8 136 79 0.1 1 74 5 137 108 0.1 1 102 6 138 76 0.1 1 74 2 139 97 0.1 1 93 4 140 46 0.1 1 43 3 141 50 0.1 1 49 1 142 69 0.1 1 66 3 143 52 0.1 1 49 3 144 30 0.1 1 28 2 145 32 0.1 1 27 5 146 64 0.1 1 56 8 147 41 0.1 1 34 7 148 113 0.1 1 102 11 149 47 0.1 1 32 15 150 176 0.1 1 16 160 151 24625 0.1 1 199 24426 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz ============================================= 3996315 sequences processed in total