SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA Library_Geoduck_MG_3_S1_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2696.49 s (30 us/read; 1.98 M reads/minute). === Summary === Total reads processed: 88,941,440 Reads with adapters: 50,629,031 (56.9%) Reads written (passing filters): 88,941,440 (100.0%) Total basepairs processed: 13,430,157,440 bp Quality-trimmed: 516,821,182 bp (3.8%) Total written (filtered): 10,822,883,249 bp (80.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 50629031 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 15.3% C: 35.8% G: 22.4% T: 26.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10740819 22235360.0 0 10740819 2 2883216 5558840.0 0 2883216 3 876631 1389710.0 0 876631 4 428102 347427.5 0 428102 5 300091 86856.9 0 300091 6 162824 21714.2 0 162824 7 174352 5428.6 0 174352 8 192916 1357.1 0 192916 9 249121 339.3 0 247908 1213 10 168134 84.8 1 160539 7595 11 230929 21.2 1 221387 9542 12 267207 5.3 1 255413 11794 13 312130 5.3 1 299434 12696 14 213034 5.3 1 204426 8608 15 302846 5.3 1 289994 12852 16 240887 5.3 1 228847 12040 17 234852 5.3 1 226509 8343 18 218700 5.3 1 210438 8262 19 140320 5.3 1 135591 4729 20 211892 5.3 1 202001 9891 21 305234 5.3 1 288808 16426 22 307747 5.3 1 296537 11210 23 233822 5.3 1 225938 7884 24 240902 5.3 1 234134 6768 25 279973 5.3 1 271379 8594 26 300986 5.3 1 290509 10477 27 363401 5.3 1 351076 12325 28 147245 5.3 1 141480 5765 29 264658 5.3 1 254130 10528 30 228810 5.3 1 222005 6805 31 171549 5.3 1 165588 5961 32 306117 5.3 1 298452 7665 33 179650 5.3 1 174397 5253 34 311089 5.3 1 301891 9198 35 463030 5.3 1 449805 13225 36 166627 5.3 1 162418 4209 37 374065 5.3 1 364921 9144 38 150371 5.3 1 146388 3983 39 217970 5.3 1 211431 6539 40 268012 5.3 1 259126 8886 41 167180 5.3 1 161973 5207 42 326977 5.3 1 317552 9425 43 489606 5.3 1 475667 13939 44 125130 5.3 1 121009 4121 45 601345 5.3 1 589060 12285 46 51836 5.3 1 48806 3030 47 288279 5.3 1 282462 5817 48 232041 5.3 1 227055 4986 49 288602 5.3 1 282315 6287 50 180243 5.3 1 175031 5212 51 232991 5.3 1 226936 6055 52 193530 5.3 1 189241 4289 53 298785 5.3 1 290922 7863 54 431689 5.3 1 420510 11179 55 488841 5.3 1 478312 10529 56 300200 5.3 1 294018 6182 57 223007 5.3 1 218284 4723 58 305256 5.3 1 298834 6422 59 300700 5.3 1 294879 5821 60 223286 5.3 1 218347 4939 61 230740 5.3 1 225737 5003 62 187265 5.3 1 183011 4254 63 300940 5.3 1 293573 7367 64 358761 5.3 1 350998 7763 65 373143 5.3 1 364738 8405 66 453347 5.3 1 443705 9642 67 398605 5.3 1 390327 8278 68 412659 5.3 1 403616 9043 69 469462 5.3 1 458745 10717 70 550178 5.3 1 537905 12273 71 881154 5.3 1 862584 18570 72 10679297 5.3 1 10616312 62985 73 2123436 5.3 1 2104474 18962 74 461073 5.3 1 455657 5416 75 166170 5.3 1 163243 2927 76 100997 5.3 1 98714 2283 77 96795 5.3 1 94701 2094 78 80577 5.3 1 78645 1932 79 71982 5.3 1 70353 1629 80 63975 5.3 1 62415 1560 81 59274 5.3 1 57741 1533 82 57183 5.3 1 55813 1370 83 64180 5.3 1 62743 1437 84 71948 5.3 1 70284 1664 85 80395 5.3 1 78668 1727 86 81442 5.3 1 79596 1846 87 80411 5.3 1 78583 1828 88 78453 5.3 1 76670 1783 89 71272 5.3 1 69682 1590 90 61015 5.3 1 59629 1386 91 50213 5.3 1 48967 1246 92 43715 5.3 1 42560 1155 93 45406 5.3 1 44261 1145 94 53143 5.3 1 51776 1367 95 64410 5.3 1 63005 1405 96 76734 5.3 1 75032 1702 97 78517 5.3 1 76762 1755 98 75342 5.3 1 73691 1651 99 70231 5.3 1 68727 1504 100 64101 5.3 1 62713 1388 101 56094 5.3 1 54918 1176 102 84263 5.3 1 83207 1056 103 45976 5.3 1 45014 962 104 44715 5.3 1 43553 1162 105 56702 5.3 1 55411 1291 106 72139 5.3 1 70616 1523 107 80442 5.3 1 78860 1582 108 77200 5.3 1 75509 1691 109 70196 5.3 1 68755 1441 110 62426 5.3 1 61045 1381 111 52310 5.3 1 51137 1173 112 42602 5.3 1 41591 1011 113 36195 5.3 1 35299 896 114 38194 5.3 1 37318 876 115 46041 5.3 1 45040 1001 116 51763 5.3 1 50730 1033 117 51633 5.3 1 50621 1012 118 50847 5.3 1 49849 998 119 43544 5.3 1 42641 903 120 38342 5.3 1 37473 869 121 36945 5.3 1 36095 850 122 36026 5.3 1 35193 833 123 35046 5.3 1 34263 783 124 28685 5.3 1 28058 627 125 8381 5.3 1 8068 313 126 2841 5.3 1 2563 278 127 1824 5.3 1 1566 258 128 1320 5.3 1 1033 287 129 792 5.3 1 541 251 130 748 5.3 1 439 309 131 565 5.3 1 300 265 132 588 5.3 1 368 220 133 377 5.3 1 137 240 134 389 5.3 1 106 283 135 296 5.3 1 72 224 136 336 5.3 1 71 265 137 214 5.3 1 30 184 138 306 5.3 1 9 297 139 280 5.3 1 9 271 140 252 5.3 1 14 238 141 337 5.3 1 18 319 142 608 5.3 1 36 572 143 933 5.3 1 21 912 144 177 5.3 1 4 173 145 249 5.3 1 10 239 146 127 5.3 1 8 119 147 221 5.3 1 3 218 148 484 5.3 1 3 481 149 184 5.3 1 7 177 150 69 5.3 1 0 69 151 81 5.3 1 0 81 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R1_001.fastq.gz ============================================= 88941440 sequences processed in total