SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_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_7_S2_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 3090.17 s (35 us/read; 1.71 M reads/minute). === Summary === Total reads processed: 88,314,076 Reads with adapters: 42,085,008 (47.7%) Reads written (passing filters): 88,314,076 (100.0%) Total basepairs processed: 13,335,425,476 bp Quality-trimmed: 580,847,327 bp (4.4%) Total written (filtered): 11,470,592,114 bp (86.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 42085008 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.3% C: 34.2% G: 23.1% T: 26.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13815390 22078519.0 0 13815390 2 2903007 5519629.8 0 2903007 3 858433 1379907.4 0 858433 4 444846 344976.9 0 444846 5 356245 86244.2 0 356245 6 88425 21561.1 0 88425 7 192578 5390.3 0 192578 8 134365 1347.6 0 134365 9 302952 336.9 0 301713 1239 10 147983 84.2 1 128845 19138 11 214261 21.1 1 195344 18917 12 257575 5.3 1 235067 22508 13 358131 5.3 1 323251 34880 14 154590 5.3 1 139441 15149 15 390204 5.3 1 352897 37307 16 301173 5.3 1 271471 29702 17 116222 5.3 1 105407 10815 18 244462 5.3 1 221166 23296 19 243108 5.3 1 224270 18838 20 158469 5.3 1 144680 13789 21 154476 5.3 1 142774 11702 22 380789 5.3 1 350660 30129 23 133812 5.3 1 122174 11638 24 502426 5.3 1 467946 34480 25 257212 5.3 1 241585 15627 26 147897 5.3 1 137502 10395 27 198670 5.3 1 186943 11727 28 354573 5.3 1 335535 19038 29 206095 5.3 1 195568 10527 30 94303 5.3 1 88247 6056 31 269195 5.3 1 256089 13106 32 153503 5.3 1 147100 6403 33 87009 5.3 1 81814 5195 34 438335 5.3 1 420537 17798 35 43851 5.3 1 39862 3989 36 259925 5.3 1 249150 10775 37 404204 5.3 1 386211 17993 38 114808 5.3 1 108521 6287 39 336591 5.3 1 324557 12034 40 63973 5.3 1 59089 4884 41 274501 5.3 1 261632 12869 42 287294 5.3 1 276699 10595 43 304894 5.3 1 294932 9962 44 144286 5.3 1 138653 5633 45 362621 5.3 1 353064 9557 46 265796 5.3 1 256904 8892 47 230798 5.3 1 224183 6615 48 261645 5.3 1 254507 7138 49 175700 5.3 1 171155 4545 50 307800 5.3 1 300542 7258 51 50823 5.3 1 48523 2300 52 196137 5.3 1 190871 5266 53 218924 5.3 1 212377 6547 54 468463 5.3 1 458870 9593 55 160927 5.3 1 155823 5104 56 325655 5.3 1 315119 10536 57 418012 5.3 1 409075 8937 58 168897 5.3 1 164897 4000 59 170877 5.3 1 167072 3805 60 173407 5.3 1 169369 4038 61 150736 5.3 1 146535 4201 62 254742 5.3 1 249322 5420 63 317446 5.3 1 311442 6004 64 116976 5.3 1 114609 2367 65 152947 5.3 1 150134 2813 66 124491 5.3 1 121807 2684 67 381882 5.3 1 376181 5701 68 81616 5.3 1 79507 2109 69 181354 5.3 1 177709 3645 70 236502 5.3 1 232200 4302 71 112714 5.3 1 110366 2348 72 176074 5.3 1 172441 3633 73 214263 5.3 1 210268 3995 74 323279 5.3 1 317611 5668 75 573931 5.3 1 564593 9338 76 5123114 5.3 1 5091744 31370 77 944898 5.3 1 935759 9139 78 165918 5.3 1 163262 2656 79 54730 5.3 1 53273 1457 80 34966 5.3 1 33856 1110 81 28604 5.3 1 27740 864 82 22339 5.3 1 21467 872 83 24071 5.3 1 23180 891 84 31098 5.3 1 30000 1098 85 37724 5.3 1 36697 1027 86 45682 5.3 1 44441 1241 87 48954 5.3 1 47620 1334 88 46094 5.3 1 44960 1134 89 40067 5.3 1 38935 1132 90 32234 5.3 1 31361 873 91 25905 5.3 1 25071 834 92 21664 5.3 1 20931 733 93 21322 5.3 1 20463 859 94 24588 5.3 1 23852 736 95 30848 5.3 1 29989 859 96 35741 5.3 1 34789 952 97 38815 5.3 1 37746 1069 98 35781 5.3 1 34738 1043 99 31719 5.3 1 30792 927 100 27260 5.3 1 26353 907 101 21446 5.3 1 20750 696 102 17268 5.3 1 16534 734 103 15585 5.3 1 14849 736 104 18416 5.3 1 17556 860 105 25870 5.3 1 24747 1123 106 33367 5.3 1 31973 1394 107 35823 5.3 1 34851 972 108 33683 5.3 1 32816 867 109 28611 5.3 1 27816 795 110 23616 5.3 1 22938 678 111 18775 5.3 1 18257 518 112 14563 5.3 1 14065 498 113 12481 5.3 1 12025 456 114 13547 5.3 1 13027 520 115 18671 5.3 1 18103 568 116 21513 5.3 1 20953 560 117 20559 5.3 1 19985 574 118 18201 5.3 1 17684 517 119 14031 5.3 1 13547 484 120 10716 5.3 1 10331 385 121 9576 5.3 1 9192 384 122 9187 5.3 1 8828 359 123 8492 5.3 1 8107 385 124 7137 5.3 1 6829 308 125 1583 5.3 1 1314 269 126 578 5.3 1 336 242 127 563 5.3 1 304 259 128 400 5.3 1 172 228 129 313 5.3 1 88 225 130 327 5.3 1 89 238 131 243 5.3 1 57 186 132 308 5.3 1 62 246 133 266 5.3 1 32 234 134 239 5.3 1 26 213 135 218 5.3 1 20 198 136 250 5.3 1 16 234 137 261 5.3 1 11 250 138 314 5.3 1 7 307 139 299 5.3 1 3 296 140 270 5.3 1 14 256 141 255 5.3 1 13 242 142 506 5.3 1 31 475 143 758 5.3 1 29 729 144 205 5.3 1 5 200 145 207 5.3 1 7 200 146 105 5.3 1 4 101 147 187 5.3 1 3 184 148 350 5.3 1 7 343 149 159 5.3 1 1 158 150 59 5.3 1 2 57 151 39 5.3 1 0 39 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R2_001.fastq.gz ============================================= 88314076 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88314076 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 277637 (0.31%)