SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_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/AD002_S9_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 5230.58 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 212,571,014 Reads with adapters: 84,686,365 (39.8%) Reads written (passing filters): 212,571,014 (100.0%) Total basepairs processed: 27,177,135,971 bp Quality-trimmed: 13,245,075 bp (0.0%) Total written (filtered): 26,838,125,885 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 84686365 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.1% C: 22.4% G: 14.6% T: 29.9% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 60674168 53142753.5 0 60674168 2 14784594 13285688.4 0 14784594 3 3967718 3321422.1 0 3967718 4 1480924 830355.5 0 1480924 5 146347 207588.9 0 146347 6 48580 51897.2 0 48580 7 33791 12974.3 0 33791 8 36656 3243.6 0 36656 9 26598 810.9 0 23963 2635 10 44418 202.7 1 29185 15233 11 38922 50.7 1 26762 12160 12 69792 12.7 1 53960 15832 13 1195 3.2 1 438 757 14 47339 3.2 1 35576 11763 15 52770 3.2 1 41608 11162 16 634 3.2 1 201 433 17 42726 3.2 1 33263 9463 18 22684 3.2 1 17428 5256 19 47567 3.2 1 36469 11098 20 31403 3.2 1 24000 7403 21 28364 3.2 1 21698 6666 22 34047 3.2 1 26354 7693 23 36561 3.2 1 28207 8354 24 65463 3.2 1 49951 15512 25 34947 3.2 1 27542 7405 26 34962 3.2 1 27304 7658 27 29006 3.2 1 21592 7414 28 53205 3.2 1 43379 9826 29 20582 3.2 1 14366 6216 30 53904 3.2 1 43886 10018 31 25572 3.2 1 18856 6716 32 104215 3.2 1 89702 14513 33 48556 3.2 1 38303 10253 34 20322 3.2 1 14286 6036 35 57948 3.2 1 48742 9206 36 17162 3.2 1 12263 4899 37 31403 3.2 1 23930 7473 38 10608 3.2 1 7550 3058 39 18784 3.2 1 13894 4890 40 6633 3.2 1 4568 2065 41 32112 3.2 1 26002 6110 42 45616 3.2 1 37841 7775 43 21704 3.2 1 16865 4839 44 37574 3.2 1 30256 7318 45 87545 3.2 1 75914 11631 46 36246 3.2 1 28464 7782 47 16572 3.2 1 12732 3840 48 80742 3.2 1 69143 11599 49 21381 3.2 1 16623 4758 50 8037 3.2 1 5550 2487 51 63171 3.2 1 53351 9820 52 96340 3.2 1 86234 10106 53 23443 3.2 1 19108 4335 54 36014 3.2 1 29600 6414 55 15334 3.2 1 12053 3281 56 10515 3.2 1 7531 2984 57 18137 3.2 1 14127 4010 58 22631 3.2 1 17766 4865 59 11751 3.2 1 8432 3319 60 10054 3.2 1 6973 3081 61 9870 3.2 1 6812 3058 62 9763 3.2 1 6789 2974 63 10788 3.2 1 7883 2905 64 17688 3.2 1 14248 3440 65 25196 3.2 1 20885 4311 66 29017 3.2 1 24067 4950 67 30511 3.2 1 25231 5280 68 31480 3.2 1 25807 5673 69 32138 3.2 1 26359 5779 70 32297 3.2 1 26434 5863 71 32854 3.2 1 26895 5959 72 32640 3.2 1 26633 6007 73 32787 3.2 1 26654 6133 74 32692 3.2 1 26640 6052 75 32484 3.2 1 26426 6058 76 32184 3.2 1 26187 5997 77 32358 3.2 1 26268 6090 78 31723 3.2 1 25744 5979 79 31696 3.2 1 25821 5875 80 31836 3.2 1 25842 5994 81 31424 3.2 1 25584 5840 82 31042 3.2 1 25270 5772 83 30875 3.2 1 25140 5735 84 30591 3.2 1 24859 5732 85 30931 3.2 1 25246 5685 86 30493 3.2 1 24853 5640 87 30152 3.2 1 24619 5533 88 29712 3.2 1 24263 5449 89 29210 3.2 1 23885 5325 90 28789 3.2 1 23402 5387 91 28484 3.2 1 23115 5369 92 28346 3.2 1 23073 5273 93 27777 3.2 1 22496 5281 94 27264 3.2 1 22205 5059 95 27108 3.2 1 22001 5107 96 26638 3.2 1 21556 5082 97 26212 3.2 1 21295 4917 98 25833 3.2 1 21100 4733 99 25454 3.2 1 20687 4767 100 24923 3.2 1 20366 4557 101 24287 3.2 1 19828 4459 102 23797 3.2 1 19329 4468 103 23126 3.2 1 18853 4273 104 22695 3.2 1 18494 4201 105 22093 3.2 1 17881 4212 106 21097 3.2 1 17034 4063 107 20219 3.2 1 16232 3987 108 19562 3.2 1 15645 3917 109 18798 3.2 1 14996 3802 110 18084 3.2 1 14372 3712 111 17805 3.2 1 14243 3562 112 17170 3.2 1 13696 3474 113 16335 3.2 1 13209 3126 114 15585 3.2 1 12555 3030 115 15021 3.2 1 12002 3019 116 14681 3.2 1 11658 3023 117 14216 3.2 1 11363 2853 118 13499 3.2 1 10813 2686 119 13000 3.2 1 10405 2595 120 12029 3.2 1 9603 2426 121 11664 3.2 1 9343 2321 122 10909 3.2 1 8712 2197 123 10511 3.2 1 8406 2105 124 9754 3.2 1 7760 1994 125 9173 3.2 1 7375 1798 126 8573 3.2 1 6946 1627 127 7964 3.2 1 6426 1538 128 6884 3.2 1 5641 1243 129 6554 3.2 1 5541 1013 130 5155 3.2 1 4404 751 131 4812 3.2 1 4172 640 132 3624 3.2 1 3207 417 133 3284 3.2 1 2958 326 134 2667 3.2 1 2388 279 135 2436 3.2 1 2207 229 136 1933 3.2 1 1774 159 137 1689 3.2 1 1566 123 138 1293 3.2 1 1168 125 139 1070 3.2 1 960 110 140 763 3.2 1 676 87 141 591 3.2 1 514 77 142 474 3.2 1 374 100 143 386 3.2 1 316 70 144 374 3.2 1 285 89 145 336 3.2 1 247 89 146 280 3.2 1 196 84 147 260 3.2 1 184 76 148 209 3.2 1 132 77 149 233 3.2 1 143 90 150 460 3.2 1 349 111 151 59702 3.2 1 58455 1247 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz ============================================= 212571014 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 212571014 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 679425 (0.32%)