SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_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_1_S3_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2897.19 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 83,562,471 Reads with adapters: 38,392,912 (45.9%) Reads written (passing filters): 83,562,471 (100.0%) Total basepairs processed: 12,617,933,121 bp Quality-trimmed: 241,837,593 bp (1.9%) Total written (filtered): 11,342,814,479 bp (89.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38392912 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.4% C: 33.7% G: 25.1% T: 24.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13870321 20890617.8 0 13870321 2 3335301 5222654.4 0 3335301 3 1043475 1305663.6 0 1043475 4 398194 326415.9 0 398194 5 278415 81604.0 0 278415 6 146118 20401.0 0 146118 7 160255 5100.2 0 160255 8 166688 1275.1 0 166688 9 205766 318.8 0 204471 1295 10 134850 79.7 1 129017 5833 11 183874 19.9 1 176793 7081 12 209435 5.0 1 201380 8055 13 253517 5.0 1 244238 9279 14 180337 5.0 1 174332 6005 15 258996 5.0 1 249336 9660 16 209555 5.0 1 201231 8324 17 190068 5.0 1 184234 5834 18 197520 5.0 1 191013 6507 19 108110 5.0 1 105012 3098 20 165276 5.0 1 158727 6549 21 210505 5.0 1 200652 9853 22 252929 5.0 1 244405 8524 23 165029 5.0 1 159499 5530 24 200834 5.0 1 195477 5357 25 222837 5.0 1 216873 5964 26 239329 5.0 1 232002 7327 27 293925 5.0 1 285727 8198 28 115347 5.0 1 111512 3835 29 196702 5.0 1 190279 6423 30 173191 5.0 1 168995 4196 31 110383 5.0 1 106998 3385 32 226587 5.0 1 221510 5077 33 137465 5.0 1 133994 3471 34 188166 5.0 1 183524 4642 35 239252 5.0 1 232636 6616 36 364315 5.0 1 355591 8724 37 102785 5.0 1 99575 3210 38 288040 5.0 1 281796 6244 39 54999 5.0 1 53323 1676 40 154448 5.0 1 150673 3775 41 191885 5.0 1 186039 5846 42 192440 5.0 1 188147 4293 43 202555 5.0 1 197703 4852 44 159796 5.0 1 156612 3184 45 453329 5.0 1 445550 7779 46 38215 5.0 1 36349 1866 47 201032 5.0 1 197434 3598 48 169680 5.0 1 166612 3068 49 203952 5.0 1 200125 3827 50 120637 5.0 1 117616 3021 51 145665 5.0 1 142275 3390 52 123054 5.0 1 120617 2437 53 180684 5.0 1 176429 4255 54 258874 5.0 1 252714 6160 55 322973 5.0 1 316754 6219 56 183280 5.0 1 179738 3542 57 149807 5.0 1 146986 2821 58 192892 5.0 1 189283 3609 59 194304 5.0 1 191017 3287 60 143274 5.0 1 140550 2724 61 132433 5.0 1 129808 2625 62 109366 5.0 1 107013 2353 63 170249 5.0 1 166484 3765 64 194641 5.0 1 190811 3830 65 201487 5.0 1 197327 4160 66 255760 5.0 1 250845 4915 67 217589 5.0 1 213440 4149 68 235836 5.0 1 231080 4756 69 246577 5.0 1 241387 5190 70 271012 5.0 1 265612 5400 71 393472 5.0 1 385928 7544 72 4243396 5.0 1 4218165 25231 73 834755 5.0 1 827481 7274 74 182416 5.0 1 180229 2187 75 74035 5.0 1 72725 1310 76 48967 5.0 1 47847 1120 77 50500 5.0 1 49387 1113 78 41173 5.0 1 40209 964 79 37506 5.0 1 36600 906 80 31703 5.0 1 30904 799 81 27904 5.0 1 27194 710 82 24980 5.0 1 24306 674 83 27330 5.0 1 26603 727 84 31648 5.0 1 30804 844 85 35461 5.0 1 34638 823 86 35257 5.0 1 34452 805 87 35427 5.0 1 34567 860 88 35041 5.0 1 34191 850 89 31687 5.0 1 30990 697 90 26319 5.0 1 25593 726 91 21452 5.0 1 20857 595 92 18055 5.0 1 17521 534 93 18279 5.0 1 17719 560 94 20868 5.0 1 20248 620 95 25493 5.0 1 24854 639 96 30556 5.0 1 29860 696 97 31023 5.0 1 30319 704 98 29547 5.0 1 28851 696 99 27291 5.0 1 26620 671 100 24215 5.0 1 23555 660 101 21225 5.0 1 20654 571 102 35197 5.0 1 34707 490 103 17220 5.0 1 16753 467 104 15509 5.0 1 15000 509 105 19433 5.0 1 18884 549 106 25150 5.0 1 24510 640 107 27422 5.0 1 26757 665 108 25314 5.0 1 24718 596 109 22005 5.0 1 21432 573 110 18929 5.0 1 18387 542 111 15129 5.0 1 14656 473 112 12063 5.0 1 11640 423 113 10585 5.0 1 10213 372 114 11785 5.0 1 11425 360 115 15067 5.0 1 14602 465 116 16848 5.0 1 16448 400 117 16323 5.0 1 15909 414 118 14611 5.0 1 14139 472 119 11623 5.0 1 11248 375 120 9061 5.0 1 8742 319 121 8552 5.0 1 8182 370 122 8236 5.0 1 7943 293 123 7738 5.0 1 7388 350 124 6343 5.0 1 6042 301 125 1532 5.0 1 1280 252 126 544 5.0 1 382 162 127 556 5.0 1 308 248 128 452 5.0 1 228 224 129 346 5.0 1 141 205 130 369 5.0 1 135 234 131 298 5.0 1 104 194 132 290 5.0 1 97 193 133 267 5.0 1 39 228 134 232 5.0 1 44 188 135 267 5.0 1 25 242 136 287 5.0 1 26 261 137 243 5.0 1 18 225 138 238 5.0 1 11 227 139 288 5.0 1 13 275 140 247 5.0 1 6 241 141 247 5.0 1 8 239 142 433 5.0 1 33 400 143 819 5.0 1 12 807 144 173 5.0 1 4 169 145 258 5.0 1 2 256 146 128 5.0 1 0 128 147 188 5.0 1 2 186 148 377 5.0 1 6 371 149 150 5.0 1 0 150 150 79 5.0 1 0 79 151 63 5.0 1 1 62 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R1_001.fastq.gz ============================================= 83562471 sequences processed in total