SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_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/NR006_S3_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 79.63 s (26 us/read; 2.28 M reads/minute). === Summary === Total reads processed: 3,031,025 Reads with adapters: 1,929,386 (63.7%) Reads written (passing filters): 3,031,025 (100.0%) Total basepairs processed: 455,473,203 bp Quality-trimmed: 59,204 bp (0.0%) Total written (filtered): 412,084,346 bp (90.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1929386 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.7% C: 25.2% G: 18.5% T: 19.2% none/other: 7.3% Overview of removed sequences length count expect max.err error counts 1 788408 757756.2 0 788408 2 151285 189439.1 0 151285 3 67064 47359.8 0 67064 4 53544 11839.9 0 53544 5 487 2960.0 0 487 6 20856 740.0 0 20856 7 19031 185.0 0 19031 8 21515 46.2 0 21515 9 19602 11.6 0 19467 135 10 20380 2.9 1 19099 1281 11 21123 0.7 1 19494 1629 12 40181 0.2 1 37607 2574 13 635 0.0 1 259 376 14 39626 0.0 1 36980 2646 15 546 0.0 1 216 330 16 40328 0.0 1 37445 2883 17 781 0.0 1 428 353 18 24020 0.0 1 22173 1847 19 64281 0.0 1 60433 3848 20 390 0.0 1 219 171 21 136 0.0 1 107 29 22 298 0.0 1 212 86 23 18040 0.0 1 16632 1408 24 47127 0.0 1 43895 3232 25 820 0.0 1 521 299 26 15602 0.0 1 14517 1085 27 14558 0.0 1 13600 958 28 317 0.0 1 213 104 29 14674 0.0 1 13589 1085 30 16895 0.0 1 15657 1238 31 23644 0.0 1 22177 1467 32 688 0.0 1 446 242 33 23967 0.0 1 22293 1674 34 1270 0.0 1 965 305 35 21680 0.0 1 20211 1469 36 10887 0.0 1 10143 744 37 243 0.0 1 157 86 38 9846 0.0 1 9114 732 39 10438 0.0 1 9648 790 40 8976 0.0 1 8310 666 41 10247 0.0 1 9296 951 42 22213 0.0 1 20655 1558 43 4212 0.0 1 3853 359 44 3399 0.0 1 3115 284 45 122 0.0 1 89 33 46 6912 0.0 1 6349 563 47 6086 0.0 1 5620 466 48 6045 0.0 1 5510 535 49 6310 0.0 1 5804 506 50 10220 0.0 1 9462 758 51 4524 0.0 1 4143 381 52 191 0.0 1 121 70 53 5734 0.0 1 5264 470 54 11519 0.0 1 10583 936 55 261 0.0 1 210 51 56 1303 0.0 1 1144 159 57 9194 0.0 1 8511 683 58 118 0.0 1 84 34 59 170 0.0 1 104 66 60 5353 0.0 1 4961 392 61 68 0.0 1 39 29 62 55 0.0 1 36 19 63 1544 0.0 1 1403 141 64 2235 0.0 1 2041 194 65 2238 0.0 1 2057 181 66 2678 0.0 1 2481 197 67 1852 0.0 1 1687 165 68 2019 0.0 1 1822 197 69 391 0.0 1 347 44 70 605 0.0 1 551 54 71 1093 0.0 1 1007 86 72 1059 0.0 1 980 79 73 1081 0.0 1 983 98 74 1093 0.0 1 991 102 75 962 0.0 1 884 78 76 906 0.0 1 823 83 77 876 0.0 1 798 78 78 823 0.0 1 723 100 79 822 0.0 1 745 77 80 790 0.0 1 713 77 81 698 0.0 1 629 69 82 635 0.0 1 575 60 83 596 0.0 1 528 68 84 583 0.0 1 530 53 85 491 0.0 1 442 49 86 475 0.0 1 424 51 87 442 0.0 1 395 47 88 480 0.0 1 412 68 89 416 0.0 1 373 43 90 372 0.0 1 332 40 91 335 0.0 1 297 38 92 347 0.0 1 300 47 93 309 0.0 1 274 35 94 312 0.0 1 265 47 95 472 0.0 1 443 29 96 279 0.0 1 253 26 97 332 0.0 1 233 99 98 520 0.0 1 407 113 99 445 0.0 1 326 119 100 435 0.0 1 249 186 101 350 0.0 1 280 70 102 357 0.0 1 182 175 103 219 0.0 1 171 48 104 248 0.0 1 222 26 105 153 0.0 1 129 24 106 144 0.0 1 127 17 107 348 0.0 1 326 22 108 186 0.0 1 156 30 109 175 0.0 1 157 18 110 163 0.0 1 148 15 111 147 0.0 1 126 21 112 146 0.0 1 137 9 113 124 0.0 1 115 9 114 124 0.0 1 112 12 115 165 0.0 1 152 13 116 161 0.0 1 142 19 117 138 0.0 1 128 10 118 144 0.0 1 132 12 119 139 0.0 1 127 12 120 132 0.0 1 114 18 121 122 0.0 1 108 14 122 147 0.0 1 137 10 123 169 0.0 1 152 17 124 133 0.0 1 126 7 125 170 0.0 1 158 12 126 123 0.0 1 109 14 127 176 0.0 1 169 7 128 143 0.0 1 135 8 129 173 0.0 1 168 5 130 186 0.0 1 169 17 131 142 0.0 1 134 8 132 129 0.0 1 123 6 133 152 0.0 1 145 7 134 164 0.0 1 158 6 135 129 0.0 1 117 12 136 152 0.0 1 140 12 137 133 0.0 1 126 7 138 125 0.0 1 119 6 139 129 0.0 1 124 5 140 75 0.0 1 66 9 141 90 0.0 1 81 9 142 137 0.0 1 125 12 143 60 0.0 1 56 4 144 50 0.0 1 42 8 145 25 0.0 1 23 2 146 51 0.0 1 45 6 147 51 0.0 1 37 14 148 107 0.0 1 79 28 149 79 0.0 1 36 43 150 395 0.0 1 14 381 151 141220 0.0 1 56 141164 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz ============================================= 3031025 sequences processed in total