SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_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/NR012_S1_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 7.24 s (26 us/read; 2.33 M reads/minute). === Summary === Total reads processed: 281,472 Reads with adapters: 121,688 (43.2%) Reads written (passing filters): 281,472 (100.0%) Total basepairs processed: 35,695,401 bp Quality-trimmed: 15,812 bp (0.0%) Total written (filtered): 34,569,512 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 121688 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.3% C: 23.7% G: 15.8% T: 26.8% none/other: 2.5% Overview of removed sequences length count expect max.err error counts 1 75815 70368.0 0 75815 2 19000 17592.0 0 19000 3 5354 4398.0 0 5354 4 2554 1099.5 0 2554 5 243 274.9 0 243 6 426 68.7 0 426 7 331 17.2 0 331 8 402 4.3 0 402 9 348 1.1 0 346 2 10 401 0.3 1 365 36 11 394 0.1 1 352 42 12 746 0.0 1 695 51 13 21 0.0 1 11 10 14 750 0.0 1 686 64 15 14 0.0 1 8 6 16 792 0.0 1 723 69 17 29 0.0 1 20 9 18 456 0.0 1 419 37 19 1132 0.0 1 1070 62 20 9 0.0 1 5 4 21 3 0.0 1 1 2 22 9 0.0 1 6 3 23 386 0.0 1 351 35 24 901 0.0 1 828 73 25 15 0.0 1 10 5 26 308 0.0 1 288 20 27 287 0.0 1 258 29 28 7 0.0 1 5 2 29 301 0.0 1 264 37 30 340 0.0 1 310 30 31 454 0.0 1 425 29 32 19 0.0 1 16 3 33 507 0.0 1 457 50 34 456 0.0 1 431 25 35 18 0.0 1 16 2 36 60 0.0 1 51 9 37 216 0.0 1 198 18 38 218 0.0 1 197 21 39 255 0.0 1 242 13 40 185 0.0 1 168 17 41 200 0.0 1 172 28 42 414 0.0 1 387 27 43 106 0.0 1 94 12 44 98 0.0 1 87 11 45 96 0.0 1 78 18 46 237 0.0 1 220 17 47 156 0.0 1 143 13 48 113 0.0 1 103 10 49 342 0.0 1 323 19 50 243 0.0 1 220 23 51 78 0.0 1 74 4 52 71 0.0 1 66 5 53 244 0.0 1 229 15 54 161 0.0 1 153 8 55 30 0.0 1 26 4 56 46 0.0 1 41 5 57 182 0.0 1 167 15 58 9 0.0 1 8 1 59 34 0.0 1 24 10 60 87 0.0 1 84 3 61 3 0.0 1 3 62 16 0.0 1 10 6 63 56 0.0 1 48 8 64 85 0.0 1 79 6 65 52 0.0 1 40 12 66 55 0.0 1 54 1 67 35 0.0 1 32 3 68 20 0.0 1 18 2 69 16 0.0 1 8 8 70 40 0.0 1 32 8 71 30 0.0 1 27 3 72 32 0.0 1 30 2 73 24 0.0 1 20 4 74 27 0.0 1 27 75 38 0.0 1 34 4 76 39 0.0 1 34 5 77 41 0.0 1 39 2 78 39 0.0 1 35 4 79 36 0.0 1 34 2 80 30 0.0 1 27 3 81 32 0.0 1 30 2 82 25 0.0 1 24 1 83 29 0.0 1 24 5 84 30 0.0 1 26 4 85 27 0.0 1 27 86 22 0.0 1 19 3 87 23 0.0 1 18 5 88 19 0.0 1 14 5 89 33 0.0 1 31 2 90 27 0.0 1 24 3 91 22 0.0 1 18 4 92 19 0.0 1 16 3 93 20 0.0 1 16 4 94 26 0.0 1 25 1 95 18 0.0 1 16 2 96 13 0.0 1 11 2 97 14 0.0 1 14 98 16 0.0 1 13 3 99 23 0.0 1 17 6 100 9 0.0 1 9 101 14 0.0 1 13 1 102 22 0.0 1 19 3 103 25 0.0 1 22 3 104 17 0.0 1 16 1 105 12 0.0 1 12 106 12 0.0 1 11 1 107 8 0.0 1 7 1 108 7 0.0 1 6 1 109 11 0.0 1 9 2 110 6 0.0 1 3 3 111 16 0.0 1 14 2 112 10 0.0 1 9 1 113 9 0.0 1 8 1 114 6 0.0 1 5 1 115 10 0.0 1 9 1 116 8 0.0 1 8 117 4 0.0 1 3 1 118 4 0.0 1 3 1 119 7 0.0 1 7 120 6 0.0 1 5 1 121 11 0.0 1 8 3 122 3 0.0 1 3 123 7 0.0 1 5 2 124 8 0.0 1 6 2 125 7 0.0 1 7 126 11 0.0 1 9 2 127 6 0.0 1 5 1 128 8 0.0 1 6 2 129 4 0.0 1 4 130 9 0.0 1 9 131 8 0.0 1 8 132 11 0.0 1 11 133 6 0.0 1 6 134 6 0.0 1 6 135 7 0.0 1 7 136 5 0.0 1 5 137 10 0.0 1 10 138 5 0.0 1 5 139 7 0.0 1 7 140 2 0.0 1 2 141 5 0.0 1 5 142 4 0.0 1 4 143 3 0.0 1 3 144 4 0.0 1 3 1 145 5 0.0 1 4 1 146 3 0.0 1 3 147 4 0.0 1 3 1 148 9 0.0 1 8 1 149 3 0.0 1 0 3 150 18 0.0 1 0 18 151 3005 0.0 1 83 2922 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz ============================================= 281472 sequences processed in total