SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.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/NR006_S3_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 80.21 s (26 us/read; 2.27 M reads/minute). === Summary === Total reads processed: 3,031,025 Reads with adapters: 1,797,618 (59.3%) Reads written (passing filters): 3,031,025 (100.0%) Total basepairs processed: 454,130,095 bp Quality-trimmed: 81,905 bp (0.0%) Total written (filtered): 432,938,122 bp (95.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1797618 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.9% C: 25.0% G: 20.4% T: 21.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 803750 757756.2 0 803750 2 159777 189439.1 0 159777 3 74983 47359.8 0 74983 4 55464 11839.9 0 55464 5 534 2960.0 0 534 6 20415 740.0 0 20415 7 19928 185.0 0 19928 8 23459 46.2 0 23459 9 17406 11.6 0 17255 151 10 20562 2.9 1 19800 762 11 19822 0.7 1 18851 971 12 39785 0.2 1 38357 1428 13 251 0.0 1 63 188 14 22463 0.0 1 21347 1116 15 35189 0.0 1 33798 1391 16 162 0.0 1 69 93 17 22058 0.0 1 21192 866 18 14401 0.0 1 13797 604 19 21417 0.0 1 20543 874 20 16595 0.0 1 15928 667 21 15273 0.0 1 14570 703 22 16562 0.0 1 15897 665 23 16572 0.0 1 15858 714 24 23886 0.0 1 22883 1003 25 15834 0.0 1 15311 523 26 15356 0.0 1 14732 624 27 9520 0.0 1 8970 550 28 23049 0.0 1 22321 728 29 4963 0.0 1 4603 360 30 21010 0.0 1 20327 683 31 6944 0.0 1 6487 457 32 40614 0.0 1 39579 1035 33 11790 0.0 1 11296 494 34 3553 0.0 1 3261 292 35 19784 0.0 1 19297 487 36 3727 0.0 1 3499 228 37 7832 0.0 1 7453 379 38 2360 0.0 1 2247 113 39 4177 0.0 1 4003 174 40 1155 0.0 1 1084 71 41 8529 0.0 1 8285 244 42 11564 0.0 1 11239 325 43 4405 0.0 1 4220 185 44 7519 0.0 1 7261 258 45 14908 0.0 1 14491 417 46 5316 0.0 1 5076 240 47 3010 0.0 1 2866 144 48 12584 0.0 1 12240 344 49 3165 0.0 1 3063 102 50 895 0.0 1 841 54 51 7922 0.0 1 7682 240 52 13903 0.0 1 13616 287 53 3428 0.0 1 3297 131 54 4044 0.0 1 3901 143 55 1734 0.0 1 1680 54 56 889 0.0 1 818 71 57 1690 0.0 1 1620 70 58 1719 0.0 1 1649 70 59 761 0.0 1 721 40 60 547 0.0 1 521 26 61 484 0.0 1 454 30 62 497 0.0 1 468 29 63 572 0.0 1 547 25 64 1256 0.0 1 1215 41 65 1584 0.0 1 1533 51 66 1636 0.0 1 1586 50 67 1562 0.0 1 1515 47 68 1413 0.0 1 1368 45 69 1431 0.0 1 1386 45 70 1373 0.0 1 1324 49 71 1279 0.0 1 1241 38 72 1137 0.0 1 1092 45 73 1089 0.0 1 1040 49 74 1049 0.0 1 1008 41 75 952 0.0 1 930 22 76 884 0.0 1 844 40 77 850 0.0 1 825 25 78 785 0.0 1 757 28 79 789 0.0 1 761 28 80 759 0.0 1 730 29 81 660 0.0 1 633 27 82 621 0.0 1 595 26 83 561 0.0 1 528 33 84 581 0.0 1 551 30 85 472 0.0 1 452 20 86 464 0.0 1 446 18 87 455 0.0 1 439 16 88 459 0.0 1 439 20 89 409 0.0 1 390 19 90 391 0.0 1 367 24 91 381 0.0 1 362 19 92 325 0.0 1 308 17 93 325 0.0 1 309 16 94 299 0.0 1 289 10 95 301 0.0 1 289 12 96 283 0.0 1 261 22 97 265 0.0 1 249 16 98 369 0.0 1 308 61 99 341 0.0 1 305 36 100 291 0.0 1 278 13 101 288 0.0 1 257 31 102 207 0.0 1 199 8 103 196 0.0 1 185 11 104 233 0.0 1 216 17 105 164 0.0 1 154 10 106 146 0.0 1 136 10 107 328 0.0 1 316 12 108 188 0.0 1 176 12 109 171 0.0 1 162 9 110 162 0.0 1 153 9 111 151 0.0 1 143 8 112 147 0.0 1 138 9 113 141 0.0 1 132 9 114 129 0.0 1 120 9 115 154 0.0 1 147 7 116 156 0.0 1 154 2 117 138 0.0 1 130 8 118 144 0.0 1 134 10 119 137 0.0 1 130 7 120 126 0.0 1 121 5 121 120 0.0 1 115 5 122 148 0.0 1 138 10 123 164 0.0 1 153 11 124 154 0.0 1 139 15 125 162 0.0 1 158 4 126 113 0.0 1 106 7 127 176 0.0 1 166 10 128 141 0.0 1 134 7 129 174 0.0 1 169 5 130 175 0.0 1 158 17 131 139 0.0 1 132 7 132 127 0.0 1 122 5 133 150 0.0 1 142 8 134 159 0.0 1 148 11 135 120 0.0 1 114 6 136 146 0.0 1 131 15 137 127 0.0 1 116 11 138 123 0.0 1 101 22 139 125 0.0 1 112 13 140 69 0.0 1 59 10 141 86 0.0 1 73 13 142 125 0.0 1 108 17 143 56 0.0 1 42 14 144 43 0.0 1 29 14 145 25 0.0 1 13 12 146 39 0.0 1 30 9 147 31 0.0 1 14 17 148 81 0.0 1 38 43 149 37 0.0 1 21 16 150 18 0.0 1 7 11 151 211 0.0 1 46 165 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz ============================================= 3031025 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 3031025 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 143798 (4.74%)