SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_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/NR014_AD014_S5_L001_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 17866.55 s (24 us/read; 2.52 M reads/minute). === Summary === Total reads processed: 750,570,443 Reads with adapters: 289,187,209 (38.5%) Reads written (passing filters): 750,570,443 (100.0%) Total basepairs processed: 88,547,063,621 bp Quality-trimmed: 51,479,249 bp (0.1%) Total written (filtered): 86,834,377,140 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 289187209 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 23.5% G: 15.1% T: 29.7% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 192909668 187642610.8 0 192909668 2 54350674 46910652.7 0 54350674 3 14030638 11727663.2 0 14030638 4 5645418 2931915.8 0 5645418 5 644053 732978.9 0 644053 6 309787 183244.7 0 309787 7 237428 45811.2 0 237428 8 281248 11452.8 0 281248 9 249313 2863.2 0 241008 8305 10 279192 715.8 1 232507 46685 11 286431 178.9 1 241423 45008 12 515773 44.7 1 463019 52754 13 18367 11.2 1 11839 6528 14 508262 11.2 1 456715 51547 15 14833 11.2 1 8724 6109 16 544414 11.2 1 480512 63902 17 23775 11.2 1 14558 9217 18 359075 11.2 1 315603 43472 19 825945 11.2 1 762424 63521 20 5665 11.2 1 3478 2187 21 4990 11.2 1 2183 2807 22 10358 11.2 1 5510 4848 23 299789 11.2 1 264190 35599 24 667172 11.2 1 605345 61827 25 19949 11.2 1 12651 7298 26 256354 11.2 1 226389 29965 27 230460 11.2 1 210212 20248 28 6568 11.2 1 3872 2696 29 245569 11.2 1 216886 28683 30 317069 11.2 1 286417 30652 31 374473 11.2 1 339859 34614 32 19468 11.2 1 12962 6506 33 450331 11.2 1 403885 46446 34 7586 11.2 1 4925 2661 35 238662 11.2 1 207824 30838 36 250935 11.2 1 221628 29307 37 254545 11.2 1 225209 29336 38 414582 11.2 1 369817 44765 39 210154 11.2 1 191129 19025 40 7717 11.2 1 4738 2979 41 255519 11.2 1 224930 30589 42 220673 11.2 1 196986 23687 43 253997 11.2 1 221561 32436 44 538821 11.2 1 489058 49763 45 109189 11.2 1 100829 8360 46 120125 11.2 1 102249 17876 47 6331 11.2 1 3868 2463 48 235082 11.2 1 208233 26849 49 198823 11.2 1 177604 21219 50 193998 11.2 1 170789 23209 51 239801 11.2 1 208357 31444 52 380896 11.2 1 343749 37147 53 166334 11.2 1 152005 14329 54 16602 11.2 1 12011 4591 55 330481 11.2 1 297411 33070 56 505188 11.2 1 464589 40599 57 31464 11.2 1 26508 4956 58 89482 11.2 1 78503 10979 59 471636 11.2 1 438787 32849 60 13294 11.2 1 9635 3659 61 31799 11.2 1 22753 9046 62 348119 11.2 1 323874 24245 63 6467 11.2 1 4271 2196 64 13543 11.2 1 8483 5060 65 105779 11.2 1 94646 11133 66 228594 11.2 1 209330 19264 67 202694 11.2 1 185615 17079 68 246807 11.2 1 228830 17977 69 144456 11.2 1 130812 13644 70 116936 11.2 1 103663 13273 71 54946 11.2 1 47030 7916 72 75718 11.2 1 67992 7726 73 114178 11.2 1 105273 8905 74 127551 11.2 1 117131 10420 75 133108 11.2 1 121830 11278 76 135663 11.2 1 124030 11633 77 135833 11.2 1 123792 12041 78 135999 11.2 1 123523 12476 79 134513 11.2 1 122024 12489 80 132353 11.2 1 119792 12561 81 131502 11.2 1 119043 12459 82 129476 11.2 1 117100 12376 83 127413 11.2 1 115100 12313 84 125209 11.2 1 113013 12196 85 124152 11.2 1 112064 12088 86 122198 11.2 1 110146 12052 87 119141 11.2 1 107493 11648 88 118327 11.2 1 106680 11647 89 114684 11.2 1 103226 11458 90 112928 11.2 1 101561 11367 91 110169 11.2 1 99211 10958 92 107113 11.2 1 96201 10912 93 105103 11.2 1 94518 10585 94 103054 11.2 1 92695 10359 95 101527 11.2 1 91241 10286 96 98938 11.2 1 88802 10136 97 96670 11.2 1 87063 9607 98 93458 11.2 1 83912 9546 99 91216 11.2 1 82070 9146 100 88277 11.2 1 79256 9021 101 84267 11.2 1 75500 8767 102 81040 11.2 1 72488 8552 103 76881 11.2 1 68764 8117 104 71322 11.2 1 63577 7745 105 66845 11.2 1 59357 7488 106 61236 11.2 1 54084 7152 107 54672 11.2 1 47874 6798 108 49926 11.2 1 43230 6696 109 43801 11.2 1 37446 6355 110 40718 11.2 1 34799 5919 111 39329 11.2 1 33521 5808 112 37285 11.2 1 31675 5610 113 36474 11.2 1 31067 5407 114 34974 11.2 1 29828 5146 115 34356 11.2 1 29518 4838 116 33052 11.2 1 28418 4634 117 32570 11.2 1 28040 4530 118 31661 11.2 1 27284 4377 119 31114 11.2 1 27029 4085 120 30169 11.2 1 26088 4081 121 29542 11.2 1 25780 3762 122 27978 11.2 1 24484 3494 123 27542 11.2 1 24306 3236 124 26034 11.2 1 22997 3037 125 27797 11.2 1 24853 2944 126 24952 11.2 1 22306 2646 127 27223 11.2 1 24604 2619 128 24870 11.2 1 22619 2251 129 44965 11.2 1 42042 2923 130 23224 11.2 1 21466 1758 131 35351 11.2 1 33515 1836 132 21416 11.2 1 20253 1163 133 23072 11.2 1 22010 1062 134 19541 11.2 1 18686 855 135 22239 11.2 1 21349 890 136 18813 11.2 1 18114 699 137 20313 11.2 1 19612 701 138 17790 11.2 1 17295 495 139 17086 11.2 1 16597 489 140 15218 11.2 1 14783 435 141 14618 11.2 1 14200 418 142 12159 11.2 1 11781 378 143 13967 11.2 1 13572 395 144 11090 11.2 1 10754 336 145 11962 11.2 1 11529 433 146 9230 11.2 1 8851 379 147 8773 11.2 1 8302 471 148 7357 11.2 1 6629 728 149 8441 11.2 1 7255 1186 150 18295 11.2 1 9802 8493 151 2054622 11.2 1 682481 1372141 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz ============================================= 750570443 sequences processed in total