SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_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/NR014_AD014_S5_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 18489.76 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 750,570,443 Reads with adapters: 299,526,533 (39.9%) Reads written (passing filters): 750,570,443 (100.0%) Total basepairs processed: 91,326,369,816 bp Quality-trimmed: 58,430,294 bp (0.1%) Total written (filtered): 89,411,521,810 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 299526533 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.5% C: 22.9% G: 15.6% T: 29.8% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 195508272 187642610.8 0 195508272 2 53701405 46910652.7 0 53701405 3 14830289 11727663.2 0 14830289 4 5884365 2931915.8 0 5884365 5 580478 732978.9 0 580478 6 433990 183244.7 0 433990 7 373366 45811.2 0 373366 8 443852 11452.8 0 443852 9 319608 2863.2 0 310462 9146 10 425138 715.8 1 356030 69108 11 405396 178.9 1 341837 63559 12 791929 44.7 1 699759 92170 13 7085 11.2 1 3337 3748 14 479779 11.2 1 414019 65760 15 666605 11.2 1 597374 69231 16 3296 11.2 1 1405 1891 17 447935 11.2 1 395018 52917 18 283150 11.2 1 249797 33353 19 479301 11.2 1 420748 58553 20 348868 11.2 1 308297 40571 21 318834 11.2 1 280791 38043 22 359445 11.2 1 319023 40422 23 383741 11.2 1 337154 46587 24 609570 11.2 1 532241 77329 25 355609 11.2 1 317427 38182 26 376193 11.2 1 333823 42370 27 287577 11.2 1 246800 40777 28 564034 11.2 1 513550 50484 29 164754 11.2 1 134266 30488 30 537878 11.2 1 487749 50129 31 235999 11.2 1 202289 33710 32 1053810 11.2 1 982245 71565 33 439075 11.2 1 388688 50387 34 143201 11.2 1 117029 26172 35 549014 11.2 1 503741 45273 36 171248 11.2 1 147222 24026 37 269301 11.2 1 234512 34789 38 138046 11.2 1 122921 15125 39 190077 11.2 1 166107 23970 40 72430 11.2 1 62897 9533 41 307972 11.2 1 280936 27036 42 435964 11.2 1 401434 34530 43 197707 11.2 1 175590 22117 44 332032 11.2 1 299779 32253 45 743685 11.2 1 691844 51841 46 293743 11.2 1 258266 35477 47 147612 11.2 1 131958 15654 48 642368 11.2 1 594726 47642 49 205842 11.2 1 185331 20511 50 69850 11.2 1 59300 10550 51 482885 11.2 1 444980 37905 52 819026 11.2 1 777011 42015 53 279581 11.2 1 258697 20884 54 371032 11.2 1 342874 28158 55 201835 11.2 1 186009 15826 56 93525 11.2 1 81149 12376 57 181125 11.2 1 164075 17050 58 201528 11.2 1 181670 19858 59 106205 11.2 1 92181 14024 60 72144 11.2 1 60589 11555 61 67276 11.2 1 56173 11103 62 73654 11.2 1 62651 11003 63 88612 11.2 1 77301 11311 64 160280 11.2 1 146493 13787 65 211526 11.2 1 194467 17059 66 230118 11.2 1 211041 19077 67 233193 11.2 1 213309 19884 68 232801 11.2 1 212622 20179 69 232837 11.2 1 212661 20176 70 230956 11.2 1 210679 20277 71 230712 11.2 1 210035 20677 72 227427 11.2 1 206864 20563 73 224834 11.2 1 204801 20033 74 220854 11.2 1 200966 19888 75 217348 11.2 1 197730 19618 76 213212 11.2 1 193853 19359 77 210130 11.2 1 191101 19029 78 207107 11.2 1 188351 18756 79 201762 11.2 1 183564 18198 80 198242 11.2 1 180336 17906 81 195772 11.2 1 178095 17677 82 191787 11.2 1 174331 17456 83 188512 11.2 1 171336 17176 84 186114 11.2 1 169107 17007 85 183104 11.2 1 166525 16579 86 180176 11.2 1 164018 16158 87 176875 11.2 1 161108 15767 88 173208 11.2 1 157369 15839 89 168365 11.2 1 153113 15252 90 163173 11.2 1 148130 15043 91 159873 11.2 1 145102 14771 92 154865 11.2 1 140836 14029 93 152411 11.2 1 138467 13944 94 148681 11.2 1 135244 13437 95 145839 11.2 1 132601 13238 96 141809 11.2 1 129026 12783 97 137914 11.2 1 125518 12396 98 133616 11.2 1 121504 12112 99 130159 11.2 1 118199 11960 100 125571 11.2 1 114128 11443 101 120631 11.2 1 109465 11166 102 114670 11.2 1 103928 10742 103 108518 11.2 1 98139 10379 104 98959 11.2 1 89090 9869 105 90807 11.2 1 81324 9483 106 80925 11.2 1 72014 8911 107 69986 11.2 1 61403 8583 108 61928 11.2 1 53842 8086 109 51721 11.2 1 44112 7609 110 47044 11.2 1 39803 7241 111 44643 11.2 1 37536 7107 112 42188 11.2 1 35304 6884 113 40737 11.2 1 34327 6410 114 39256 11.2 1 33071 6185 115 38548 11.2 1 32442 6106 116 37109 11.2 1 31381 5728 117 36299 11.2 1 30884 5415 118 35146 11.2 1 29963 5183 119 34570 11.2 1 29658 4912 120 33134 11.2 1 28543 4591 121 32475 11.2 1 28113 4362 122 30765 11.2 1 26673 4092 123 30432 11.2 1 26520 3912 124 28512 11.2 1 24762 3750 125 30138 11.2 1 26594 3544 126 27221 11.2 1 24034 3187 127 29101 11.2 1 26126 2975 128 26261 11.2 1 23747 2514 129 46487 11.2 1 44023 2464 130 23963 11.2 1 22173 1790 131 35973 11.2 1 34287 1686 132 21567 11.2 1 20281 1286 133 23281 11.2 1 22074 1207 134 19695 11.2 1 18575 1120 135 22376 11.2 1 21283 1093 136 18882 11.2 1 17760 1122 137 20353 11.2 1 19196 1157 138 17856 11.2 1 16607 1249 139 17077 11.2 1 15902 1175 140 15173 11.2 1 13937 1236 141 14561 11.2 1 13203 1358 142 12110 11.2 1 10652 1458 143 13944 11.2 1 12264 1680 144 11169 11.2 1 9336 1833 145 11834 11.2 1 9757 2077 146 9067 11.2 1 7040 2027 147 8590 11.2 1 6651 1939 148 6792 11.2 1 5016 1776 149 7588 11.2 1 5615 1973 150 14895 11.2 1 12078 2817 151 701267 11.2 1 683500 17767 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz ============================================= 750570443 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 750570443 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4761104 (0.63%)