SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_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_L002_R1_001_val_1.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 21050.32 s (24 us/read; 2.51 M reads/minute). === Summary === Total reads processed: 882,029,208 Reads with adapters: 346,789,678 (39.3%) Reads written (passing filters): 882,029,208 (100.0%) Total basepairs processed: 106,455,935,222 bp Quality-trimmed: 52,712,555 bp (0.0%) Total written (filtered): 104,195,667,043 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 346789678 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 23.5% G: 15.0% T: 29.7% none/other: 0.8% Overview of removed sequences length count expect max.err error counts 1 232624048 220507302.0 0 232624048 2 63171145 55126825.5 0 63171145 3 16364041 13781706.4 0 16364041 4 6416328 3445426.6 0 6416328 5 712237 861356.6 0 712237 6 338291 215339.2 0 338291 7 256798 53834.8 0 256798 8 299385 13458.7 0 299385 9 269984 3364.7 0 260119 9865 10 307146 841.2 1 253539 53607 11 315713 210.3 1 264417 51296 12 562598 52.6 1 503159 59439 13 19773 13.1 1 12157 7616 14 552117 13.1 1 496927 55190 15 16227 13.1 1 8906 7321 16 596749 13.1 1 526191 70558 17 27757 13.1 1 16526 11231 18 393755 13.1 1 344817 48938 19 910749 13.1 1 842499 68250 20 6613 13.1 1 4009 2604 21 6467 13.1 1 2594 3873 22 12592 13.1 1 6281 6311 23 329115 13.1 1 286324 42791 24 753373 13.1 1 681700 71673 25 22850 13.1 1 14018 8832 26 290173 13.1 1 254343 35830 27 256563 13.1 1 234123 22440 28 7769 13.1 1 4433 3336 29 277229 13.1 1 243555 33674 30 351843 13.1 1 315504 36339 31 436338 13.1 1 392748 43590 32 23439 13.1 1 14948 8491 33 525669 13.1 1 466840 58829 34 9392 13.1 1 5925 3467 35 281455 13.1 1 240818 40637 36 294552 13.1 1 257293 37259 37 297296 13.1 1 259132 38164 38 493224 13.1 1 434828 58396 39 243583 13.1 1 220510 23073 40 9618 13.1 1 5695 3923 41 303835 13.1 1 265494 38341 42 254452 13.1 1 224354 30098 43 308613 13.1 1 264246 44367 44 654339 13.1 1 589647 64692 45 128733 13.1 1 118218 10515 46 140916 13.1 1 118230 22686 47 7614 13.1 1 4438 3176 48 271899 13.1 1 238607 33292 49 234233 13.1 1 207020 27213 50 249540 13.1 1 216599 32941 51 294191 13.1 1 248847 45344 52 475128 13.1 1 423307 51821 53 212764 13.1 1 192266 20498 54 20848 13.1 1 14202 6646 55 373944 13.1 1 327143 46801 56 656108 13.1 1 595438 60670 57 35360 13.1 1 28048 7312 58 102150 13.1 1 84835 17315 59 650539 13.1 1 597527 53012 60 16480 13.1 1 11648 4832 61 38073 13.1 1 25058 13015 62 443604 13.1 1 406917 36687 63 7517 13.1 1 4909 2608 64 13872 13.1 1 7818 6054 65 151378 13.1 1 133918 17460 66 259795 13.1 1 232048 27747 67 261332 13.1 1 232395 28937 68 305222 13.1 1 274651 30571 69 238490 13.1 1 212414 26076 70 300674 13.1 1 271942 28732 71 60371 13.1 1 47219 13152 72 78053 13.1 1 66578 11475 73 145094 13.1 1 131164 13930 74 168443 13.1 1 152721 15722 75 178369 13.1 1 161202 17167 76 183267 13.1 1 165070 18197 77 185332 13.1 1 166059 19273 78 185669 13.1 1 166032 19637 79 184689 13.1 1 164958 19731 80 183758 13.1 1 163905 19853 81 182961 13.1 1 162933 20028 82 181147 13.1 1 161071 20076 83 179647 13.1 1 159268 20379 84 179288 13.1 1 158666 20622 85 176739 13.1 1 156220 20519 86 175156 13.1 1 154930 20226 87 172269 13.1 1 152575 19694 88 171226 13.1 1 151246 19980 89 167198 13.1 1 147679 19519 90 165543 13.1 1 145909 19634 91 162119 13.1 1 142744 19375 92 159287 13.1 1 140282 19005 93 157565 13.1 1 138859 18706 94 155466 13.1 1 136859 18607 95 151105 13.1 1 133065 18040 96 150049 13.1 1 132085 17964 97 146097 13.1 1 128574 17523 98 143252 13.1 1 125855 17397 99 139784 13.1 1 122884 16900 100 136912 13.1 1 120038 16874 101 132459 13.1 1 116012 16447 102 129407 13.1 1 113040 16367 103 123250 13.1 1 107686 15564 104 116965 13.1 1 101765 15200 105 111444 13.1 1 96645 14799 106 104382 13.1 1 89841 14541 107 95932 13.1 1 82076 13856 108 90857 13.1 1 76743 14114 109 82767 13.1 1 69467 13300 110 78135 13.1 1 65334 12801 111 75752 13.1 1 63276 12476 112 73108 13.1 1 61040 12068 113 70775 13.1 1 59264 11511 114 68614 13.1 1 57411 11203 115 67336 13.1 1 56534 10802 116 64527 13.1 1 54287 10240 117 63276 13.1 1 53412 9864 118 61181 13.1 1 51519 9662 119 59921 13.1 1 50861 9060 120 57524 13.1 1 48564 8960 121 56580 13.1 1 48099 8481 122 53484 13.1 1 45411 8073 123 51725 13.1 1 44332 7393 124 48421 13.1 1 41518 6903 125 50894 13.1 1 44326 6568 126 46143 13.1 1 39934 6209 127 48871 13.1 1 42933 5938 128 43008 13.1 1 38170 4838 129 72254 13.1 1 66995 5259 130 39005 13.1 1 35333 3672 131 55946 13.1 1 52525 3421 132 34239 13.1 1 31874 2365 133 36791 13.1 1 34839 1952 134 29888 13.1 1 28301 1587 135 32842 13.1 1 31413 1429 136 27536 13.1 1 26434 1102 137 28779 13.1 1 27737 1042 138 24740 13.1 1 23988 752 139 23461 13.1 1 22794 667 140 20629 13.1 1 20112 517 141 19394 13.1 1 18916 478 142 15752 13.1 1 15304 448 143 18237 13.1 1 17814 423 144 14377 13.1 1 13941 436 145 15679 13.1 1 15212 467 146 11999 13.1 1 11562 437 147 11281 13.1 1 10783 498 148 9039 13.1 1 8390 649 149 10320 13.1 1 9341 979 150 16689 13.1 1 10308 6381 151 2792571 13.1 1 930915 1861656 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz ============================================= 882029208 sequences processed in total