SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_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/NR014_AD014_S5_L002_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 21417.12 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 882,029,208 Reads with adapters: 357,804,367 (40.6%) Reads written (passing filters): 882,029,208 (100.0%) Total basepairs processed: 109,686,944,991 bp Quality-trimmed: 57,793,498 bp (0.1%) Total written (filtered): 107,213,258,754 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 357804367 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 23.0% G: 15.5% T: 29.8% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 235099366 220507302.0 0 235099366 2 62543836 55126825.5 0 62543836 3 17144245 13781706.4 0 17144245 4 6646447 3445426.6 0 6646447 5 639554 861356.6 0 639554 6 474891 215339.2 0 474891 7 405448 53834.8 0 405448 8 466848 13458.7 0 466848 9 348446 3364.7 0 337673 10773 10 461105 841.2 1 386657 74448 11 439665 210.3 1 373444 66221 12 854670 52.6 1 764149 90521 13 7135 13.1 1 2811 4324 14 514702 13.1 1 447955 66747 15 722304 13.1 1 657406 64898 16 3921 13.1 1 1665 2256 17 483893 13.1 1 430625 53268 18 311726 13.1 1 280786 30940 19 508462 13.1 1 447409 61053 20 376124 13.1 1 336875 39249 21 359883 13.1 1 322088 37795 22 398674 13.1 1 356521 42153 23 416959 13.1 1 370051 46908 24 611113 13.1 1 529458 81655 25 410127 13.1 1 370095 40032 26 415762 13.1 1 375188 40574 27 327612 13.1 1 286723 40889 28 609543 13.1 1 556927 52616 29 205545 13.1 1 171345 34200 30 596568 13.1 1 542203 54365 31 263996 13.1 1 228833 35163 32 1289400 13.1 1 1212993 76407 33 512660 13.1 1 459500 53160 34 184716 13.1 1 153208 31508 35 692795 13.1 1 644767 48028 36 158296 13.1 1 131258 27038 37 342624 13.1 1 302501 40123 38 97006 13.1 1 81760 15246 39 183704 13.1 1 157551 26153 40 45254 13.1 1 35800 9454 41 355563 13.1 1 324511 31052 42 528472 13.1 1 488465 40007 43 208242 13.1 1 182929 25313 44 390129 13.1 1 351993 38136 45 1128825 13.1 1 1066223 62602 46 345095 13.1 1 302774 42321 47 117084 13.1 1 100592 16492 48 873716 13.1 1 814718 58998 49 169284 13.1 1 146835 22449 50 52750 13.1 1 40938 11812 51 646744 13.1 1 599590 47154 52 1193783 13.1 1 1142866 50917 53 250287 13.1 1 227517 22770 54 380803 13.1 1 348438 32365 55 138543 13.1 1 122337 16206 56 90468 13.1 1 75051 15417 57 169985 13.1 1 149829 20156 58 203858 13.1 1 180530 23328 59 93592 13.1 1 77303 16289 60 78787 13.1 1 63686 15101 61 82444 13.1 1 67562 14882 62 79746 13.1 1 65366 14380 63 94126 13.1 1 79609 14517 64 179996 13.1 1 162738 17258 65 257597 13.1 1 235879 21718 66 285315 13.1 1 261166 24149 67 292126 13.1 1 266275 25851 68 295475 13.1 1 268387 27088 69 295990 13.1 1 268443 27547 70 296714 13.1 1 268419 28295 71 300117 13.1 1 271207 28910 72 295102 13.1 1 266729 28373 73 297780 13.1 1 269028 28752 74 291630 13.1 1 263445 28185 75 287606 13.1 1 259336 28270 76 282934 13.1 1 254551 28383 77 279808 13.1 1 251854 27954 78 276410 13.1 1 248663 27747 79 271068 13.1 1 243712 27356 80 266965 13.1 1 240369 26596 81 264294 13.1 1 238046 26248 82 260238 13.1 1 233644 26594 83 258826 13.1 1 232425 26401 84 255117 13.1 1 229078 26039 85 252997 13.1 1 227278 25719 86 250320 13.1 1 224751 25569 87 246703 13.1 1 221934 24769 88 243894 13.1 1 219163 24731 89 237391 13.1 1 212725 24666 90 232269 13.1 1 207825 24444 91 227208 13.1 1 203062 24146 92 222180 13.1 1 198614 23566 93 219038 13.1 1 195701 23337 94 215630 13.1 1 192779 22851 95 212171 13.1 1 189594 22577 96 208724 13.1 1 186441 22283 97 203591 13.1 1 181707 21884 98 198733 13.1 1 177288 21445 99 195082 13.1 1 174344 20738 100 190416 13.1 1 169973 20443 101 185717 13.1 1 165304 20413 102 177447 13.1 1 157905 19542 103 169476 13.1 1 150354 19122 104 158041 13.1 1 139594 18447 105 149050 13.1 1 130821 18229 106 137972 13.1 1 120204 17768 107 124510 13.1 1 107417 17093 108 115302 13.1 1 98640 16662 109 103287 13.1 1 87118 16169 110 95710 13.1 1 80359 15351 111 92391 13.1 1 77278 15113 112 88978 13.1 1 74373 14605 113 86338 13.1 1 72405 13933 114 83339 13.1 1 69681 13658 115 81009 13.1 1 68155 12854 116 78418 13.1 1 65893 12525 117 76604 13.1 1 64480 12124 118 73600 13.1 1 61978 11622 119 72003 13.1 1 60976 11027 120 68625 13.1 1 57886 10739 121 67484 13.1 1 57305 10179 122 63641 13.1 1 53989 9652 123 61549 13.1 1 52545 9004 124 57810 13.1 1 49218 8592 125 59751 13.1 1 51688 8063 126 54119 13.1 1 46626 7493 127 56196 13.1 1 49390 6806 128 48450 13.1 1 43017 5433 129 77040 13.1 1 72208 4832 130 41906 13.1 1 38198 3708 131 58208 13.1 1 55170 3038 132 35365 13.1 1 33000 2365 133 37604 13.1 1 35650 1954 134 30524 13.1 1 28823 1701 135 33388 13.1 1 31868 1520 136 27789 13.1 1 26293 1496 137 28933 13.1 1 27576 1357 138 24891 13.1 1 23429 1462 139 23476 13.1 1 22117 1359 140 20658 13.1 1 19184 1474 141 19395 13.1 1 17726 1669 142 15659 13.1 1 13873 1786 143 18154 13.1 1 16108 2046 144 14333 13.1 1 12303 2030 145 15517 13.1 1 12894 2623 146 11673 13.1 1 9220 2453 147 10903 13.1 1 8531 2372 148 8478 13.1 1 6288 2190 149 9455 13.1 1 6948 2507 150 11337 13.1 1 8415 2922 151 948058 13.1 1 929339 18719 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz ============================================= 882029208 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 882029208 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5672977 (0.64%)