SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_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_3_S1_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2762.49 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 88,941,440 Reads with adapters: 50,557,832 (56.8%) Reads written (passing filters): 88,941,440 (100.0%) Total basepairs processed: 13,430,157,440 bp Quality-trimmed: 817,901,180 bp (6.1%) Total written (filtered): 10,526,515,424 bp (78.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 50557832 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 15.0% C: 36.6% G: 22.3% T: 26.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12102841 22235360.0 0 12102841 2 2391957 5558840.0 0 2391957 3 704014 1389710.0 0 704014 4 455591 347427.5 0 455591 5 345251 86856.9 0 345251 6 81488 21714.2 0 81488 7 180140 5428.6 0 180140 8 123502 1357.1 0 123502 9 310834 339.3 0 309842 992 10 114893 84.8 1 97438 17455 11 281746 21.2 1 255544 26202 12 245722 5.3 1 222682 23040 13 356413 5.3 1 320163 36250 14 135736 5.3 1 120635 15101 15 391698 5.3 1 351844 39854 16 272643 5.3 1 241119 31524 17 129881 5.3 1 116556 13325 18 239054 5.3 1 212999 26055 19 271998 5.3 1 247814 24184 20 168031 5.3 1 151910 16121 21 188448 5.3 1 173052 15396 22 395187 5.3 1 361084 34103 23 155232 5.3 1 141379 13853 24 533386 5.3 1 492217 41169 25 290378 5.3 1 270257 20121 26 153242 5.3 1 140952 12290 27 231867 5.3 1 216439 15428 28 390044 5.3 1 366683 23361 29 225393 5.3 1 212347 13046 30 143974 5.3 1 134430 9544 31 296372 5.3 1 279613 16759 32 235990 5.3 1 224928 11062 33 321040 5.3 1 307150 13890 34 143159 5.3 1 135599 7560 35 277226 5.3 1 265485 11741 36 226287 5.3 1 216569 9718 37 223010 5.3 1 213816 9194 38 359798 5.3 1 346337 13461 39 112910 5.3 1 105841 7069 40 355835 5.3 1 343458 12377 41 161130 5.3 1 153974 7156 42 261534 5.3 1 253881 7653 43 234303 5.3 1 226171 8132 44 244133 5.3 1 236223 7910 45 422777 5.3 1 410467 12310 46 296231 5.3 1 285560 10671 47 264373 5.3 1 256775 7598 48 274577 5.3 1 266398 8179 49 212398 5.3 1 206326 6072 50 341689 5.3 1 332576 9113 51 88988 5.3 1 85199 3789 52 237057 5.3 1 229743 7314 53 303740 5.3 1 294502 9238 54 624564 5.3 1 610862 13702 55 175759 5.3 1 169184 6575 56 407889 5.3 1 395556 12333 57 528052 5.3 1 516522 11530 58 230360 5.3 1 224543 5817 59 183603 5.3 1 179115 4488 60 265039 5.3 1 258888 6151 61 211479 5.3 1 206057 5422 62 312441 5.3 1 305492 6949 63 441351 5.3 1 433069 8282 64 163490 5.3 1 159931 3559 65 201579 5.3 1 197463 4116 66 193377 5.3 1 188529 4848 67 487211 5.3 1 477782 9429 68 125512 5.3 1 121892 3620 69 251167 5.3 1 245913 5254 70 313636 5.3 1 307800 5836 71 170362 5.3 1 166502 3860 72 267450 5.3 1 261407 6043 73 344621 5.3 1 337473 7148 74 518975 5.3 1 508825 10150 75 898294 5.3 1 880531 17763 76 10607721 5.3 1 10542674 65047 77 1892842 5.3 1 1873852 18990 78 325694 5.3 1 320679 5015 79 93750 5.3 1 91417 2333 80 53885 5.3 1 52053 1832 81 46978 5.3 1 45620 1358 82 38534 5.3 1 37196 1338 83 42265 5.3 1 40841 1424 84 58325 5.3 1 56350 1975 85 67543 5.3 1 65782 1761 86 83063 5.3 1 80837 2226 87 89502 5.3 1 87180 2322 88 86122 5.3 1 84194 1928 89 73197 5.3 1 71564 1633 90 61360 5.3 1 59707 1653 91 50131 5.3 1 48824 1307 92 43514 5.3 1 42267 1247 93 43500 5.3 1 42107 1393 94 50322 5.3 1 49081 1241 95 62030 5.3 1 60591 1439 96 72189 5.3 1 70524 1665 97 77922 5.3 1 76034 1888 98 73215 5.3 1 71294 1921 99 65787 5.3 1 63986 1801 100 58494 5.3 1 56792 1702 101 47077 5.3 1 45781 1296 102 38926 5.3 1 37661 1265 103 35991 5.3 1 34764 1227 104 41487 5.3 1 39846 1641 105 55113 5.3 1 53213 1900 106 70052 5.3 1 67538 2514 107 75976 5.3 1 74127 1849 108 73714 5.3 1 72064 1650 109 66456 5.3 1 65022 1434 110 57312 5.3 1 56062 1250 111 47748 5.3 1 46657 1091 112 38827 5.3 1 37888 939 113 32164 5.3 1 31369 795 114 33636 5.3 1 32845 791 115 41023 5.3 1 40089 934 116 47155 5.3 1 46125 1030 117 47742 5.3 1 46704 1038 118 46422 5.3 1 45435 987 119 40578 5.3 1 39739 839 120 35223 5.3 1 34440 783 121 33922 5.3 1 33156 766 122 32911 5.3 1 32153 758 123 31413 5.3 1 30688 725 124 26227 5.3 1 25686 541 125 7658 5.3 1 7294 364 126 2683 5.3 1 2432 251 127 1777 5.3 1 1488 289 128 1301 5.3 1 978 323 129 724 5.3 1 469 255 130 708 5.3 1 427 281 131 523 5.3 1 272 251 132 607 5.3 1 342 265 133 389 5.3 1 109 280 134 362 5.3 1 114 248 135 361 5.3 1 69 292 136 290 5.3 1 74 216 137 269 5.3 1 36 233 138 306 5.3 1 20 286 139 249 5.3 1 11 238 140 304 5.3 1 17 287 141 390 5.3 1 25 365 142 564 5.3 1 67 497 143 717 5.3 1 37 680 144 174 5.3 1 5 169 145 201 5.3 1 4 197 146 128 5.3 1 0 128 147 211 5.3 1 6 205 148 324 5.3 1 9 315 149 161 5.3 1 3 158 150 80 5.3 1 3 77 151 39 5.3 1 1 38 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R2_001.fastq.gz ============================================= 88941440 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88941440 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 294236 (0.33%)