SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_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/NR012_S1_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8.52 s (26 us/read; 2.30 M reads/minute). === Summary === Total reads processed: 326,252 Reads with adapters: 139,337 (42.7%) Reads written (passing filters): 326,252 (100.0%) Total basepairs processed: 42,562,422 bp Quality-trimmed: 18,976 bp (0.0%) Total written (filtered): 41,698,391 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 139337 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.2% C: 23.0% G: 16.3% T: 28.4% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 90369 81563.0 0 90369 2 21799 20390.8 0 21799 3 6520 5097.7 0 6520 4 2800 1274.4 0 2800 5 171 318.6 0 171 6 409 79.7 0 409 7 410 19.9 0 410 8 426 5.0 0 426 9 296 1.2 0 293 3 10 393 0.3 1 365 28 11 373 0.1 1 327 46 12 713 0.0 1 666 47 13 1 0.0 1 1 14 417 0.0 1 385 32 15 651 0.0 1 606 45 16 4 0.0 1 2 2 17 417 0.0 1 387 30 18 271 0.0 1 253 18 19 440 0.0 1 414 26 20 340 0.0 1 332 8 21 291 0.0 1 273 18 22 366 0.0 1 341 25 23 319 0.0 1 299 20 24 493 0.0 1 459 34 25 339 0.0 1 303 36 26 319 0.0 1 302 17 27 190 0.0 1 175 15 28 444 0.0 1 430 14 29 123 0.0 1 107 16 30 446 0.0 1 422 24 31 180 0.0 1 156 24 32 875 0.0 1 837 38 33 307 0.0 1 287 20 34 94 0.0 1 85 9 35 482 0.0 1 454 28 36 93 0.0 1 84 9 37 215 0.0 1 203 12 38 67 0.0 1 64 3 39 102 0.0 1 93 9 40 35 0.0 1 31 4 41 180 0.0 1 171 9 42 278 0.0 1 265 13 43 122 0.0 1 114 8 44 173 0.0 1 158 15 45 360 0.0 1 338 22 46 177 0.0 1 165 12 47 85 0.0 1 77 8 48 420 0.0 1 397 23 49 99 0.0 1 95 4 50 38 0.0 1 28 10 51 242 0.0 1 218 24 52 450 0.0 1 439 11 53 126 0.0 1 119 7 54 140 0.0 1 129 11 55 65 0.0 1 62 3 56 46 0.0 1 38 8 57 71 0.0 1 65 6 58 90 0.0 1 86 4 59 36 0.0 1 31 5 60 23 0.0 1 21 2 61 20 0.0 1 16 4 62 24 0.0 1 21 3 63 30 0.0 1 25 5 64 37 0.0 1 34 3 65 67 0.0 1 60 7 66 79 0.0 1 71 8 67 89 0.0 1 83 6 68 91 0.0 1 82 9 69 72 0.0 1 69 3 70 79 0.0 1 68 11 71 72 0.0 1 57 15 72 73 0.0 1 68 5 73 72 0.0 1 63 9 74 61 0.0 1 54 7 75 81 0.0 1 75 6 76 71 0.0 1 62 9 77 68 0.0 1 62 6 78 65 0.0 1 59 6 79 56 0.0 1 49 7 80 66 0.0 1 59 7 81 57 0.0 1 51 6 82 60 0.0 1 53 7 83 48 0.0 1 41 7 84 47 0.0 1 41 6 85 61 0.0 1 52 9 86 47 0.0 1 40 7 87 41 0.0 1 36 5 88 60 0.0 1 56 4 89 49 0.0 1 43 6 90 54 0.0 1 52 2 91 51 0.0 1 49 2 92 50 0.0 1 43 7 93 52 0.0 1 47 5 94 49 0.0 1 37 12 95 38 0.0 1 34 4 96 36 0.0 1 33 3 97 53 0.0 1 48 5 98 40 0.0 1 32 8 99 34 0.0 1 28 6 100 33 0.0 1 26 7 101 34 0.0 1 29 5 102 33 0.0 1 28 5 103 26 0.0 1 22 4 104 27 0.0 1 20 7 105 25 0.0 1 23 2 106 31 0.0 1 26 5 107 23 0.0 1 21 2 108 17 0.0 1 15 2 109 25 0.0 1 23 2 110 20 0.0 1 15 5 111 19 0.0 1 14 5 112 30 0.0 1 24 6 113 19 0.0 1 18 1 114 27 0.0 1 18 9 115 26 0.0 1 23 3 116 20 0.0 1 17 3 117 20 0.0 1 17 3 118 28 0.0 1 18 10 119 27 0.0 1 24 3 120 15 0.0 1 12 3 121 15 0.0 1 12 3 122 19 0.0 1 12 7 123 20 0.0 1 14 6 124 6 0.0 1 4 2 125 16 0.0 1 14 2 126 13 0.0 1 12 1 127 17 0.0 1 15 2 128 8 0.0 1 6 2 129 8 0.0 1 8 130 15 0.0 1 14 1 131 14 0.0 1 14 132 8 0.0 1 7 1 133 9 0.0 1 9 134 15 0.0 1 12 3 135 8 0.0 1 7 1 136 5 0.0 1 5 137 10 0.0 1 9 1 138 7 0.0 1 7 139 8 0.0 1 8 140 5 0.0 1 5 141 3 0.0 1 2 1 142 4 0.0 1 3 1 143 4 0.0 1 2 2 144 2 0.0 1 2 145 2 0.0 1 1 1 146 4 0.0 1 2 2 147 2 0.0 1 2 148 8 0.0 1 5 3 150 4 0.0 1 3 1 151 132 0.0 1 122 10 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz ============================================= 326252 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 326252 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5128 (1.57%)