SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_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/NR015_AD015_S6_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 7061.45 s (25 us/read; 2.43 M reads/minute). === Summary === Total reads processed: 286,345,514 Reads with adapters: 115,866,451 (40.5%) Reads written (passing filters): 286,345,514 (100.0%) Total basepairs processed: 35,998,085,991 bp Quality-trimmed: 19,015,689 bp (0.1%) Total written (filtered): 35,401,915,461 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 115866451 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.7% C: 23.1% G: 15.2% T: 29.8% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 79078292 71586378.5 0 79078292 2 20457949 17896594.6 0 20457949 3 5667589 4474148.7 0 5667589 4 2136345 1118537.2 0 2136345 5 203396 279634.3 0 203396 6 132501 69908.6 0 132501 7 111365 17477.1 0 111365 8 128366 4369.3 0 128366 9 94532 1092.3 0 90994 3538 10 126018 273.1 1 105952 20066 11 117446 68.3 1 100812 16634 12 229409 17.1 1 207524 21885 13 1726 4.3 1 637 1089 14 137420 4.3 1 121594 15826 15 195930 4.3 1 179871 16059 16 1019 4.3 1 406 613 17 129235 4.3 1 116497 12738 18 83174 4.3 1 75604 7570 19 134882 4.3 1 120454 14428 20 102012 4.3 1 92451 9561 21 94539 4.3 1 85162 9377 22 104963 4.3 1 94978 9985 23 109241 4.3 1 97982 11259 24 169194 4.3 1 149865 19329 25 108190 4.3 1 98765 9425 26 106700 4.3 1 97468 9232 27 72292 4.3 1 63329 8963 28 159462 4.3 1 147411 12051 29 47180 4.3 1 39638 7542 30 153244 4.3 1 140978 12266 31 63196 4.3 1 55159 8037 32 317234 4.3 1 300225 17009 33 121994 4.3 1 109974 12020 34 43615 4.3 1 36635 6980 35 170310 4.3 1 159614 10696 36 39610 4.3 1 33583 6027 37 87306 4.3 1 77969 9337 38 24050 4.3 1 20856 3194 39 45657 4.3 1 39827 5830 40 11498 4.3 1 9445 2053 41 86757 4.3 1 79909 6848 42 126694 4.3 1 117946 8748 43 49611 4.3 1 44116 5495 44 91218 4.3 1 83312 7906 45 219772 4.3 1 207168 12604 46 80363 4.3 1 71838 8525 47 41363 4.3 1 37265 4098 48 199800 4.3 1 187096 12704 49 51044 4.3 1 45831 5213 50 15676 4.3 1 13062 2614 51 148760 4.3 1 138677 10083 52 266390 4.3 1 255506 10884 53 63589 4.3 1 58598 4991 54 90051 4.3 1 83057 6994 55 36487 4.3 1 32986 3501 56 21520 4.3 1 18377 3143 57 40871 4.3 1 36643 4228 58 47319 4.3 1 42462 4857 59 22625 4.3 1 19152 3473 60 17420 4.3 1 14369 3051 61 17831 4.3 1 14783 3048 62 17975 4.3 1 15025 2950 63 21863 4.3 1 18777 3086 64 41409 4.3 1 37784 3625 65 56629 4.3 1 52276 4353 66 61832 4.3 1 56984 4848 67 62658 4.3 1 57537 5121 68 62434 4.3 1 56987 5447 69 62709 4.3 1 57086 5623 70 62901 4.3 1 57266 5635 71 63182 4.3 1 57483 5699 72 61596 4.3 1 55910 5686 73 61973 4.3 1 56417 5556 74 60575 4.3 1 54925 5650 75 59734 4.3 1 54144 5590 76 58840 4.3 1 53256 5584 77 58095 4.3 1 52527 5568 78 56618 4.3 1 51156 5462 79 55726 4.3 1 50288 5438 80 55092 4.3 1 49744 5348 81 53834 4.3 1 48554 5280 82 53585 4.3 1 48277 5308 83 52377 4.3 1 47209 5168 84 51678 4.3 1 46445 5233 85 51400 4.3 1 46389 5011 86 50090 4.3 1 45163 4927 87 49563 4.3 1 44686 4877 88 49536 4.3 1 44418 5118 89 54300 4.3 1 43261 11039 90 46966 4.3 1 41887 5079 91 45879 4.3 1 41024 4855 92 44543 4.3 1 39873 4670 93 43755 4.3 1 39186 4569 94 42755 4.3 1 38214 4541 95 42335 4.3 1 37965 4370 96 41082 4.3 1 36743 4339 97 40279 4.3 1 36050 4229 98 39428 4.3 1 35127 4301 99 38622 4.3 1 34464 4158 100 37168 4.3 1 33149 4019 101 35893 4.3 1 31952 3941 102 34270 4.3 1 30464 3806 103 33129 4.3 1 29302 3827 104 30511 4.3 1 26863 3648 105 28506 4.3 1 24942 3564 106 26155 4.3 1 22782 3373 107 23714 4.3 1 20265 3449 108 21008 4.3 1 17830 3178 109 18868 4.3 1 15779 3089 110 17607 4.3 1 14520 3087 111 16874 4.3 1 13908 2966 112 16298 4.3 1 13432 2866 113 16100 4.3 1 13251 2849 114 15299 4.3 1 12620 2679 115 15136 4.3 1 12454 2682 116 14617 4.3 1 12112 2505 117 13972 4.3 1 11656 2316 118 13701 4.3 1 11408 2293 119 13361 4.3 1 11090 2271 120 12786 4.3 1 10659 2127 121 12428 4.3 1 10405 2023 122 11591 4.3 1 9643 1948 123 11405 4.3 1 9595 1810 124 10712 4.3 1 9030 1682 125 10763 4.3 1 9166 1597 126 10062 4.3 1 8468 1594 127 10400 4.3 1 9011 1389 128 8928 4.3 1 7828 1100 129 12877 4.3 1 11900 977 130 7703 4.3 1 6939 764 131 10433 4.3 1 9779 654 132 6733 4.3 1 6237 496 133 7084 4.3 1 6711 373 134 5808 4.3 1 5437 371 135 6472 4.3 1 6149 323 136 5338 4.3 1 5038 300 137 5793 4.3 1 5496 297 138 4805 4.3 1 4489 316 139 4583 4.3 1 4269 314 140 4150 4.3 1 3832 318 141 3861 4.3 1 3532 329 142 3205 4.3 1 2860 345 143 3735 4.3 1 3317 418 144 2991 4.3 1 2562 429 145 3152 4.3 1 2627 525 146 2370 4.3 1 1827 543 147 2265 4.3 1 1773 492 148 1796 4.3 1 1247 549 149 1873 4.3 1 1345 528 150 2305 4.3 1 1737 568 151 228767 4.3 1 224062 4705 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz ============================================= 286345514 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 286345514 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1343740 (0.47%)