SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_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_6_S5_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2605.73 s (35 us/read; 1.69 M reads/minute). === Summary === Total reads processed: 73,610,508 Reads with adapters: 34,531,336 (46.9%) Reads written (passing filters): 73,610,508 (100.0%) Total basepairs processed: 11,115,186,708 bp Quality-trimmed: 493,115,597 bp (4.4%) Total written (filtered): 9,607,718,782 bp (86.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 34531336 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.2% C: 34.2% G: 23.7% T: 25.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12164809 18402627.0 0 12164809 2 2460932 4600656.8 0 2460932 3 728552 1150164.2 0 728552 4 359916 287541.0 0 359916 5 279786 71885.3 0 279786 6 68028 17971.3 0 68028 7 150411 4492.8 0 150411 8 100927 1123.2 0 100927 9 233433 280.8 0 232415 1018 10 111315 70.2 1 96495 14820 11 164501 17.6 1 149749 14752 12 193744 4.4 1 176581 17163 13 277141 4.4 1 249324 27817 14 115994 4.4 1 104380 11614 15 302492 4.4 1 272877 29615 16 230694 4.4 1 207676 23018 17 88270 4.4 1 79931 8339 18 190873 4.4 1 172390 18483 19 185039 4.4 1 170654 14385 20 122969 4.4 1 112168 10801 21 116784 4.4 1 107713 9071 22 294009 4.4 1 270610 23399 23 102074 4.4 1 93065 9009 24 389547 4.4 1 362165 27382 25 196340 4.4 1 184212 12128 26 112092 4.4 1 104179 7913 27 150664 4.4 1 141680 8984 28 274805 4.4 1 259720 15085 29 163866 4.4 1 155380 8486 30 74321 4.4 1 69427 4894 31 194339 4.4 1 184731 9608 32 116377 4.4 1 111425 4952 33 65516 4.4 1 61663 3853 34 336323 4.4 1 322627 13696 35 33434 4.4 1 30315 3119 36 199110 4.4 1 190961 8149 37 314927 4.4 1 300656 14271 38 86329 4.4 1 81442 4887 39 258989 4.4 1 249915 9074 40 47772 4.4 1 44321 3451 41 209697 4.4 1 199902 9795 42 221086 4.4 1 213093 7993 43 235755 4.4 1 228133 7622 44 110648 4.4 1 106346 4302 45 280672 4.4 1 272906 7766 46 205643 4.4 1 198827 6816 47 177230 4.4 1 172233 4997 48 205148 4.4 1 199584 5564 49 135485 4.4 1 131942 3543 50 239675 4.4 1 234010 5665 51 39624 4.4 1 37716 1908 52 150612 4.4 1 146653 3959 53 168171 4.4 1 163308 4863 54 370553 4.4 1 363169 7384 55 119427 4.4 1 115552 3875 56 245761 4.4 1 238473 7288 57 320546 4.4 1 313794 6752 58 130334 4.4 1 127167 3167 59 132351 4.4 1 129474 2877 60 133192 4.4 1 130031 3161 61 114555 4.4 1 111446 3109 62 198186 4.4 1 193904 4282 63 245945 4.4 1 241338 4607 64 91699 4.4 1 89744 1955 65 118346 4.4 1 116078 2268 66 98150 4.4 1 96080 2070 67 297293 4.4 1 292886 4407 68 63685 4.4 1 61951 1734 69 141067 4.4 1 138358 2709 70 184352 4.4 1 181206 3146 71 86386 4.4 1 84479 1907 72 137311 4.4 1 134540 2771 73 167952 4.4 1 164779 3173 74 251865 4.4 1 247453 4412 75 450167 4.4 1 442872 7295 76 4130506 4.4 1 4105472 25034 77 765948 4.4 1 758540 7408 78 133936 4.4 1 131859 2077 79 43971 4.4 1 42827 1144 80 27103 4.4 1 26206 897 81 22516 4.4 1 21791 725 82 17644 4.4 1 17028 616 83 18841 4.4 1 18158 683 84 24838 4.4 1 23969 869 85 30169 4.4 1 29346 823 86 36546 4.4 1 35546 1000 87 39797 4.4 1 38756 1041 88 37128 4.4 1 36183 945 89 32141 4.4 1 31286 855 90 26115 4.4 1 25379 736 91 21126 4.4 1 20516 610 92 17388 4.4 1 16814 574 93 16699 4.4 1 16074 625 94 19418 4.4 1 18821 597 95 24671 4.4 1 23971 700 96 28934 4.4 1 28161 773 97 31377 4.4 1 30502 875 98 29002 4.4 1 28172 830 99 25798 4.4 1 25023 775 100 21968 4.4 1 21248 720 101 17019 4.4 1 16424 595 102 13764 4.4 1 13201 563 103 12490 4.4 1 11929 561 104 14699 4.4 1 14001 698 105 20374 4.4 1 19479 895 106 26538 4.4 1 25576 962 107 28904 4.4 1 28076 828 108 27927 4.4 1 27165 762 109 23842 4.4 1 23136 706 110 19421 4.4 1 18829 592 111 15099 4.4 1 14631 468 112 12109 4.4 1 11683 426 113 9886 4.4 1 9490 396 114 10807 4.4 1 10443 364 115 14232 4.4 1 13799 433 116 17052 4.4 1 16560 492 117 16312 4.4 1 15836 476 118 14707 4.4 1 14271 436 119 11459 4.4 1 11034 425 120 8656 4.4 1 8297 359 121 7898 4.4 1 7522 376 122 7580 4.4 1 7256 324 123 7134 4.4 1 6795 339 124 5533 4.4 1 5234 299 125 1330 4.4 1 1133 197 126 508 4.4 1 304 204 127 473 4.4 1 242 231 128 340 4.4 1 138 202 129 286 4.4 1 69 217 130 295 4.4 1 68 227 131 284 4.4 1 60 224 132 336 4.4 1 75 261 133 233 4.4 1 26 207 134 234 4.4 1 22 212 135 195 4.4 1 9 186 136 258 4.4 1 24 234 137 183 4.4 1 13 170 138 265 4.4 1 6 259 139 248 4.4 1 8 240 140 246 4.4 1 10 236 141 262 4.4 1 7 255 142 423 4.4 1 16 407 143 620 4.4 1 20 600 144 184 4.4 1 10 174 145 188 4.4 1 7 181 146 110 4.4 1 3 107 147 201 4.4 1 4 197 148 337 4.4 1 8 329 149 148 4.4 1 2 146 150 73 4.4 1 0 73 151 41 4.4 1 0 41 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R2_001.fastq.gz ============================================= 73610508 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 73610508 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 221723 (0.30%)