SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_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/NR012_S1_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.48 s (26 us/read; 2.31 M reads/minute). === Summary === Total reads processed: 326,252 Reads with adapters: 140,395 (43.0%) Reads written (passing filters): 326,252 (100.0%) Total basepairs processed: 41,596,018 bp Quality-trimmed: 15,103 bp (0.0%) Total written (filtered): 40,182,403 bp (96.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 140395 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.8% C: 23.3% G: 15.5% T: 27.4% none/other: 3.0% Overview of removed sequences length count expect max.err error counts 1 89057 81563.0 0 89057 2 21691 20390.8 0 21691 3 6146 5097.7 0 6146 4 2757 1274.4 0 2757 5 208 318.6 0 208 6 391 79.7 0 391 7 349 19.9 0 349 8 371 5.0 0 371 9 332 1.2 0 327 5 10 366 0.3 1 334 32 11 354 0.1 1 331 23 12 685 0.0 1 644 41 13 17 0.0 1 12 5 14 670 0.0 1 629 41 15 12 0.0 1 6 6 16 719 0.0 1 672 47 17 24 0.0 1 18 6 18 430 0.0 1 401 29 19 1193 0.0 1 1140 53 20 4 0.0 1 3 1 21 3 0.0 1 0 3 22 10 0.0 1 6 4 23 335 0.0 1 305 30 24 840 0.0 1 795 45 25 23 0.0 1 18 5 26 324 0.0 1 298 26 27 263 0.0 1 244 19 28 1 0.0 1 0 1 29 279 0.0 1 257 22 30 328 0.0 1 297 31 31 474 0.0 1 448 26 32 15 0.0 1 9 6 33 498 0.0 1 460 38 34 453 0.0 1 429 24 35 34 0.0 1 30 4 36 70 0.0 1 62 8 37 206 0.0 1 190 16 38 233 0.0 1 226 7 39 231 0.0 1 216 15 40 180 0.0 1 165 15 41 237 0.0 1 218 19 42 398 0.0 1 371 27 43 102 0.0 1 89 13 44 87 0.0 1 70 17 45 113 0.0 1 95 18 46 178 0.0 1 161 17 47 171 0.0 1 156 15 48 141 0.0 1 120 21 49 406 0.0 1 380 26 50 244 0.0 1 236 8 51 89 0.0 1 83 6 52 91 0.0 1 80 11 53 260 0.0 1 237 23 54 197 0.0 1 192 5 55 40 0.0 1 27 13 56 88 0.0 1 75 13 57 191 0.0 1 185 6 58 6 0.0 1 4 2 59 54 0.0 1 45 9 60 82 0.0 1 75 7 61 7 0.0 1 6 1 62 19 0.0 1 13 6 63 63 0.0 1 56 7 64 91 0.0 1 81 10 65 71 0.0 1 63 8 66 71 0.0 1 61 10 67 75 0.0 1 63 12 68 49 0.0 1 43 6 69 17 0.0 1 15 2 70 35 0.0 1 33 2 71 46 0.0 1 44 2 72 41 0.0 1 40 1 73 44 0.0 1 39 5 74 40 0.0 1 32 8 75 57 0.0 1 51 6 76 53 0.0 1 49 4 77 54 0.0 1 49 5 78 44 0.0 1 41 3 79 37 0.0 1 35 2 80 57 0.0 1 49 8 81 47 0.0 1 38 9 82 52 0.0 1 49 3 83 36 0.0 1 29 7 84 46 0.0 1 34 12 85 56 0.0 1 48 8 86 47 0.0 1 40 7 87 32 0.0 1 28 4 88 49 0.0 1 41 8 89 44 0.0 1 35 9 90 41 0.0 1 33 8 91 38 0.0 1 33 5 92 41 0.0 1 35 6 93 42 0.0 1 36 6 94 32 0.0 1 27 5 95 28 0.0 1 23 5 96 29 0.0 1 28 1 97 41 0.0 1 35 6 98 35 0.0 1 26 9 99 23 0.0 1 21 2 100 25 0.0 1 22 3 101 33 0.0 1 29 4 102 19 0.0 1 18 1 103 26 0.0 1 21 5 104 17 0.0 1 14 3 105 30 0.0 1 25 5 106 26 0.0 1 20 6 107 18 0.0 1 18 108 20 0.0 1 14 6 109 17 0.0 1 16 1 110 14 0.0 1 11 3 111 15 0.0 1 14 1 112 20 0.0 1 16 4 113 17 0.0 1 12 5 114 17 0.0 1 9 8 115 21 0.0 1 18 3 116 16 0.0 1 11 5 117 14 0.0 1 11 3 118 13 0.0 1 11 2 119 24 0.0 1 21 3 120 12 0.0 1 9 3 121 10 0.0 1 6 4 122 17 0.0 1 12 5 123 11 0.0 1 9 2 124 6 0.0 1 3 3 125 12 0.0 1 9 3 126 14 0.0 1 12 2 127 14 0.0 1 11 3 128 6 0.0 1 6 129 9 0.0 1 7 2 130 13 0.0 1 11 2 131 14 0.0 1 13 1 132 7 0.0 1 7 133 9 0.0 1 9 134 14 0.0 1 13 1 135 7 0.0 1 6 1 136 5 0.0 1 5 137 10 0.0 1 10 138 6 0.0 1 6 139 8 0.0 1 8 140 5 0.0 1 5 141 3 0.0 1 3 142 5 0.0 1 4 1 143 4 0.0 1 4 144 2 0.0 1 2 145 3 0.0 1 2 1 146 4 0.0 1 4 147 4 0.0 1 2 2 148 9 0.0 1 8 1 149 3 0.0 1 1 2 150 23 0.0 1 4 19 151 4243 0.0 1 117 4126 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz ============================================= 326252 sequences processed in total