SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_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_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 91.64 s (26 us/read; 2.31 M reads/minute). === Summary === Total reads processed: 3,532,417 Reads with adapters: 2,146,057 (60.8%) Reads written (passing filters): 3,532,417 (100.0%) Total basepairs processed: 522,802,866 bp Quality-trimmed: 102,517 bp (0.0%) Total written (filtered): 493,335,822 bp (94.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2146057 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 27.5% G: 20.7% T: 20.0% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 1 962828 883104.2 0 962828 2 190615 220776.1 0 190615 3 79318 55194.0 0 79318 4 61991 13798.5 0 61991 5 878 3449.6 0 878 6 24256 862.4 0 24256 7 21651 215.6 0 21651 8 24057 53.9 0 24057 9 22585 13.5 0 22500 85 10 22526 3.4 1 21612 914 11 23516 0.8 1 22109 1407 12 44734 0.2 1 42931 1803 13 915 0.1 1 541 374 14 43908 0.1 1 41920 1988 15 629 0.1 1 342 287 16 45177 0.1 1 42939 2238 17 992 0.1 1 649 343 18 26506 0.1 1 25049 1457 19 72561 0.1 1 69795 2766 20 462 0.1 1 263 199 21 116 0.1 1 93 23 22 353 0.1 1 232 121 23 20249 0.1 1 19187 1062 24 53005 0.1 1 50663 2342 25 791 0.1 1 527 264 26 17722 0.1 1 16903 819 27 16734 0.1 1 16040 694 28 327 0.1 1 222 105 29 16504 0.1 1 15682 822 30 18747 0.1 1 17875 872 31 26015 0.1 1 25060 955 32 648 0.1 1 440 208 33 27918 0.1 1 26622 1296 34 326 0.1 1 210 116 35 12569 0.1 1 12057 512 36 12619 0.1 1 12021 598 37 13184 0.1 1 12533 651 38 21713 0.1 1 20828 885 39 339 0.1 1 246 93 40 10499 0.1 1 10040 459 41 9561 0.1 1 9084 477 42 11337 0.1 1 10789 548 43 9078 0.1 1 8480 598 44 23113 0.1 1 22033 1080 45 4765 0.1 1 4517 248 46 3889 0.1 1 3598 291 47 597 0.1 1 398 199 48 39522 0.1 1 38097 1425 49 12892 0.1 1 12326 566 50 1792 0.1 1 1603 189 51 9666 0.1 1 9248 418 52 6354 0.1 1 6086 268 53 740 0.1 1 658 82 54 247 0.1 1 216 31 55 3374 0.1 1 3241 133 56 1493 0.1 1 1419 74 57 137 0.1 1 114 23 58 524 0.1 1 470 54 59 965 0.1 1 894 71 60 223 0.1 1 184 39 61 416 0.1 1 387 29 62 2071 0.1 1 1977 94 63 195 0.1 1 170 25 64 461 0.1 1 425 36 65 562 0.1 1 520 42 66 1783 0.1 1 1723 60 67 320 0.1 1 285 35 68 845 0.1 1 795 50 69 1033 0.1 1 974 59 70 1298 0.1 1 1227 71 71 382 0.1 1 338 44 72 162 0.1 1 143 19 73 419 0.1 1 400 19 74 737 0.1 1 699 38 75 940 0.1 1 884 56 76 991 0.1 1 942 49 77 930 0.1 1 877 53 78 909 0.1 1 857 52 79 883 0.1 1 825 58 80 831 0.1 1 784 47 81 759 0.1 1 714 45 82 727 0.1 1 679 48 83 645 0.1 1 611 34 84 585 0.1 1 548 37 85 543 0.1 1 505 38 86 507 0.1 1 465 42 87 472 0.1 1 439 33 88 457 0.1 1 432 25 89 410 0.1 1 381 29 90 403 0.1 1 371 32 91 387 0.1 1 355 32 92 362 0.1 1 333 29 93 280 0.1 1 260 20 94 317 0.1 1 296 21 95 291 0.1 1 264 27 96 284 0.1 1 256 28 97 233 0.1 1 215 18 98 248 0.1 1 232 16 99 230 0.1 1 214 16 100 227 0.1 1 206 21 101 194 0.1 1 178 16 102 185 0.1 1 168 17 103 184 0.1 1 162 22 104 182 0.1 1 166 16 105 119 0.1 1 109 10 106 126 0.1 1 115 11 107 154 0.1 1 136 18 108 142 0.1 1 123 19 109 138 0.1 1 130 8 110 132 0.1 1 112 20 111 118 0.1 1 108 10 112 85 0.1 1 74 11 113 148 0.1 1 137 11 114 91 0.1 1 85 6 115 98 0.1 1 86 12 116 101 0.1 1 93 8 117 76 0.1 1 69 7 118 91 0.1 1 86 5 119 83 0.1 1 77 6 120 99 0.1 1 92 7 121 82 0.1 1 73 9 122 87 0.1 1 82 5 123 75 0.1 1 69 6 124 79 0.1 1 71 8 125 92 0.1 1 82 10 126 158 0.1 1 138 20 127 119 0.1 1 112 7 128 165 0.1 1 151 14 129 147 0.1 1 139 8 130 130 0.1 1 124 6 131 111 0.1 1 106 5 132 152 0.1 1 144 8 133 99 0.1 1 91 8 134 149 0.1 1 140 9 135 105 0.1 1 101 4 136 125 0.1 1 121 4 137 167 0.1 1 159 8 138 107 0.1 1 105 2 139 118 0.1 1 114 4 140 89 0.1 1 84 5 141 53 0.1 1 51 2 142 108 0.1 1 103 5 143 61 0.1 1 57 4 144 46 0.1 1 44 2 145 53 0.1 1 49 4 146 99 0.1 1 91 8 147 59 0.1 1 46 13 148 177 0.1 1 169 8 149 66 0.1 1 52 14 150 129 0.1 1 16 113 151 35017 0.1 1 286 34731 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz ============================================= 3532417 sequences processed in total