SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R2_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_2_S4_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2891.36 s (35 us/read; 1.71 M reads/minute). === Summary === Total reads processed: 82,486,730 Reads with adapters: 38,987,648 (47.3%) Reads written (passing filters): 82,486,730 (100.0%) Total basepairs processed: 12,455,496,230 bp Quality-trimmed: 633,017,461 bp (5.1%) Total written (filtered): 10,655,835,190 bp (85.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38987648 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.5% C: 34.5% G: 23.1% T: 25.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13910710 20621682.5 0 13910710 2 2695279 5155420.6 0 2695279 3 770577 1288855.2 0 770577 4 390113 322213.8 0 390113 5 299924 80553.4 0 299924 6 73228 20138.4 0 73228 7 160155 5034.6 0 160155 8 107901 1258.6 0 107901 9 247142 314.7 0 246070 1072 10 120703 78.7 1 104350 16353 11 175993 19.7 1 159643 16350 12 206721 4.9 1 187703 19018 13 298053 4.9 1 267467 30586 14 125653 4.9 1 112694 12959 15 325134 4.9 1 292269 32865 16 248621 4.9 1 222514 26107 17 95064 4.9 1 85766 9298 18 204755 4.9 1 183993 20762 19 201420 4.9 1 184892 16528 20 131627 4.9 1 119500 12127 21 125858 4.9 1 115771 10087 22 316712 4.9 1 290900 25812 23 109276 4.9 1 99224 10052 24 418959 4.9 1 388236 30723 25 213351 4.9 1 199865 13486 26 120373 4.9 1 111536 8837 27 162959 4.9 1 152944 10015 28 296398 4.9 1 279878 16520 29 175517 4.9 1 166199 9318 30 80658 4.9 1 75275 5383 31 210048 4.9 1 199508 10540 32 125298 4.9 1 119761 5537 33 71195 4.9 1 66812 4383 34 363227 4.9 1 347637 15590 35 36608 4.9 1 32874 3734 36 215646 4.9 1 206249 9397 37 338986 4.9 1 322990 15996 38 96014 4.9 1 90530 5484 39 279139 4.9 1 269049 10090 40 52571 4.9 1 48553 4018 41 230935 4.9 1 219825 11110 42 238023 4.9 1 228797 9226 43 258892 4.9 1 250155 8737 44 120071 4.9 1 115118 4953 45 305797 4.9 1 296950 8847 46 226089 4.9 1 218256 7833 47 192737 4.9 1 187055 5682 48 223263 4.9 1 216787 6476 49 148310 4.9 1 144121 4189 50 264029 4.9 1 257290 6739 51 44237 4.9 1 42021 2216 52 168160 4.9 1 163244 4916 53 186692 4.9 1 180913 5779 54 409214 4.9 1 400223 8991 55 133371 4.9 1 128894 4477 56 274187 4.9 1 265261 8926 57 353998 4.9 1 346144 7854 58 143566 4.9 1 140034 3532 59 146730 4.9 1 143317 3413 60 147040 4.9 1 143374 3666 61 128603 4.9 1 124891 3712 62 222973 4.9 1 218043 4930 63 275007 4.9 1 269512 5495 64 103158 4.9 1 100902 2256 65 133161 4.9 1 130669 2492 66 109562 4.9 1 107151 2411 67 328924 4.9 1 323700 5224 68 70562 4.9 1 68568 1994 69 156552 4.9 1 153358 3194 70 207285 4.9 1 203518 3767 71 98837 4.9 1 96597 2240 72 155917 4.9 1 152323 3594 73 191980 4.9 1 188075 3905 74 289460 4.9 1 284064 5396 75 518213 4.9 1 509442 8771 76 4949229 4.9 1 4918275 30954 77 912962 4.9 1 903824 9138 78 159126 4.9 1 156517 2609 79 51275 4.9 1 49892 1383 80 31376 4.9 1 30308 1068 81 26207 4.9 1 25352 855 82 20721 4.9 1 19819 902 83 22063 4.9 1 21219 844 84 29535 4.9 1 28484 1051 85 35047 4.9 1 34033 1014 86 42921 4.9 1 41648 1273 87 45531 4.9 1 44334 1197 88 43008 4.9 1 41926 1082 89 36863 4.9 1 35874 989 90 30007 4.9 1 29099 908 91 24226 4.9 1 23410 816 92 20240 4.9 1 19484 756 93 20103 4.9 1 19351 752 94 23388 4.9 1 22651 737 95 29024 4.9 1 28203 821 96 33995 4.9 1 33024 971 97 36351 4.9 1 35363 988 98 33941 4.9 1 32966 975 99 30349 4.9 1 29392 957 100 27084 4.9 1 26122 962 101 20717 4.9 1 19967 750 102 17063 4.9 1 16392 671 103 15358 4.9 1 14644 714 104 17857 4.9 1 17025 832 105 25376 4.9 1 24303 1073 106 32854 4.9 1 31455 1399 107 35690 4.9 1 34681 1009 108 33331 4.9 1 32446 885 109 28674 4.9 1 27886 788 110 23983 4.9 1 23268 715 111 19187 4.9 1 18599 588 112 15553 4.9 1 14990 563 113 12743 4.9 1 12222 521 114 13806 4.9 1 13269 537 115 18519 4.9 1 17949 570 116 21697 4.9 1 21071 626 117 20834 4.9 1 20249 585 118 19233 4.9 1 18681 552 119 15360 4.9 1 14867 493 120 12174 4.9 1 11732 442 121 11091 4.9 1 10673 418 122 10559 4.9 1 10131 428 123 9844 4.9 1 9475 369 124 8126 4.9 1 7815 311 125 1999 4.9 1 1754 245 126 866 4.9 1 617 249 127 635 4.9 1 373 262 128 493 4.9 1 277 216 129 371 4.9 1 140 231 130 392 4.9 1 177 215 131 317 4.9 1 103 214 132 389 4.9 1 141 248 133 295 4.9 1 59 236 134 284 4.9 1 52 232 135 247 4.9 1 33 214 136 256 4.9 1 37 219 137 234 4.9 1 20 214 138 292 4.9 1 20 272 139 271 4.9 1 9 262 140 256 4.9 1 17 239 141 302 4.9 1 23 279 142 478 4.9 1 27 451 143 632 4.9 1 27 605 144 185 4.9 1 4 181 145 208 4.9 1 4 204 146 142 4.9 1 2 140 147 218 4.9 1 3 215 148 311 4.9 1 8 303 149 159 4.9 1 1 158 150 66 4.9 1 0 66 151 48 4.9 1 0 48 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R2_001.fastq.gz ============================================= 82486730 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82486730 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 280399 (0.34%)