SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_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/AD002_S9_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 4136.23 s (25 us/read; 2.42 M reads/minute). === Summary === Total reads processed: 166,519,549 Reads with adapters: 64,336,761 (38.6%) Reads written (passing filters): 166,519,549 (100.0%) Total basepairs processed: 20,806,009,128 bp Quality-trimmed: 12,672,889 bp (0.1%) Total written (filtered): 20,606,066,844 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64336761 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.0% C: 22.5% G: 14.6% T: 29.8% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 46320342 41629887.2 0 46320342 2 11729062 10407471.8 0 11729062 3 3131394 2601868.0 0 3131394 4 1193082 650467.0 0 1193082 5 125066 162616.7 0 125066 6 31913 40654.2 0 31913 7 21845 10163.5 0 21845 8 22466 2540.9 0 22466 9 16214 635.2 0 14145 2069 10 28137 158.8 1 17439 10698 11 22555 39.7 1 15567 6988 12 42264 9.9 1 32388 9876 13 661 2.5 1 252 409 14 28072 2.5 1 20831 7241 15 31160 2.5 1 24417 6743 16 383 2.5 1 115 268 17 24954 2.5 1 18991 5963 18 13631 2.5 1 10359 3272 19 28189 2.5 1 21318 6871 20 18450 2.5 1 13935 4515 21 15196 2.5 1 11701 3495 22 19651 2.5 1 14996 4655 23 21752 2.5 1 16404 5348 24 40107 2.5 1 29978 10129 25 18750 2.5 1 14580 4170 26 18519 2.5 1 14350 4169 27 14830 2.5 1 10978 3852 28 29641 2.5 1 23843 5798 29 9716 2.5 1 6627 3089 30 29481 2.5 1 23634 5847 31 13670 2.5 1 9881 3789 32 51895 2.5 1 43576 8319 33 24414 2.5 1 18797 5617 34 8902 2.5 1 6076 2826 35 29279 2.5 1 23981 5298 36 10624 2.5 1 7727 2897 37 15397 2.5 1 11525 3872 38 8278 2.5 1 6292 1986 39 11562 2.5 1 8638 2924 40 5567 2.5 1 4069 1498 41 17152 2.5 1 13742 3410 42 23546 2.5 1 19042 4504 43 12652 2.5 1 9789 2863 44 19653 2.5 1 15410 4243 45 36962 2.5 1 30323 6639 46 18823 2.5 1 14422 4401 47 11178 2.5 1 8633 2545 48 36958 2.5 1 30588 6370 49 14327 2.5 1 11252 3075 50 5729 2.5 1 3947 1782 51 29652 2.5 1 24002 5650 52 44916 2.5 1 38911 6005 53 15569 2.5 1 12618 2951 54 20470 2.5 1 16407 4063 55 12026 2.5 1 9700 2326 56 6551 2.5 1 4773 1778 57 11696 2.5 1 9080 2616 58 13830 2.5 1 10710 3120 59 7683 2.5 1 5618 2065 60 5817 2.5 1 3898 1919 61 4974 2.5 1 3438 1536 62 5588 2.5 1 3870 1718 63 6329 2.5 1 4654 1675 64 9893 2.5 1 7791 2102 65 13175 2.5 1 10559 2616 66 14511 2.5 1 11692 2819 67 15084 2.5 1 12069 3015 68 15405 2.5 1 12128 3277 69 15754 2.5 1 12484 3270 70 15554 2.5 1 12293 3261 71 15695 2.5 1 12342 3353 72 15542 2.5 1 12261 3281 73 15911 2.5 1 12488 3423 74 15564 2.5 1 12295 3269 75 15370 2.5 1 12091 3279 76 15235 2.5 1 12023 3212 77 15186 2.5 1 11947 3239 78 14886 2.5 1 11638 3248 79 14938 2.5 1 11741 3197 80 14749 2.5 1 11564 3185 81 14257 2.5 1 11136 3121 82 14380 2.5 1 11319 3061 83 14226 2.5 1 11240 2986 84 14050 2.5 1 11075 2975 85 14041 2.5 1 11082 2959 86 13664 2.5 1 10701 2963 87 13612 2.5 1 10731 2881 88 13323 2.5 1 10438 2885 89 13177 2.5 1 10433 2744 90 12972 2.5 1 10190 2782 91 12706 2.5 1 9910 2796 92 12299 2.5 1 9703 2596 93 12161 2.5 1 9545 2616 94 11979 2.5 1 9442 2537 95 11751 2.5 1 9172 2579 96 11612 2.5 1 9161 2451 97 11434 2.5 1 9052 2382 98 10985 2.5 1 8714 2271 99 10710 2.5 1 8346 2364 100 10595 2.5 1 8333 2262 101 10225 2.5 1 8010 2215 102 9958 2.5 1 7869 2089 103 9684 2.5 1 7551 2133 104 9139 2.5 1 7086 2053 105 8751 2.5 1 6828 1923 106 8325 2.5 1 6414 1911 107 7751 2.5 1 5910 1841 108 7293 2.5 1 5567 1726 109 6982 2.5 1 5289 1693 110 6537 2.5 1 4931 1606 111 6361 2.5 1 4812 1549 112 6064 2.5 1 4553 1511 113 5782 2.5 1 4332 1450 114 5544 2.5 1 4201 1343 115 5196 2.5 1 3928 1268 116 5079 2.5 1 3833 1246 117 4888 2.5 1 3754 1134 118 4690 2.5 1 3571 1119 119 4561 2.5 1 3506 1055 120 4166 2.5 1 3208 958 121 3912 2.5 1 2949 963 122 3756 2.5 1 2849 907 123 3499 2.5 1 2677 822 124 3279 2.5 1 2478 801 125 3078 2.5 1 2378 700 126 2873 2.5 1 2201 672 127 2645 2.5 1 2035 610 128 2353 2.5 1 1889 464 129 2192 2.5 1 1820 372 130 1761 2.5 1 1460 301 131 1690 2.5 1 1438 252 132 1293 2.5 1 1114 179 133 1195 2.5 1 1033 162 134 981 2.5 1 873 108 135 940 2.5 1 841 99 136 772 2.5 1 667 105 137 701 2.5 1 627 74 138 560 2.5 1 501 59 139 486 2.5 1 422 64 140 410 2.5 1 356 54 141 340 2.5 1 284 56 142 259 2.5 1 203 56 143 273 2.5 1 211 62 144 226 2.5 1 161 65 145 247 2.5 1 183 64 146 185 2.5 1 128 57 147 178 2.5 1 123 55 148 127 2.5 1 68 59 149 178 2.5 1 114 64 150 712 2.5 1 592 120 151 43146 2.5 1 42014 1132 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz ============================================= 166519549 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 166519549 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 577240 (0.35%)