SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_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_6_S5_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2510.85 s (34 us/read; 1.76 M reads/minute). === Summary === Total reads processed: 73,610,508 Reads with adapters: 34,027,761 (46.2%) Reads written (passing filters): 73,610,508 (100.0%) Total basepairs processed: 11,115,186,708 bp Quality-trimmed: 200,453,105 bp (1.8%) Total written (filtered): 9,890,564,008 bp (89.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 34027761 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.8% C: 33.1% G: 23.6% T: 26.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10419042 18402627.0 0 10419042 2 2972643 4600656.8 0 2972643 3 908699 1150164.2 0 908699 4 357980 287541.0 0 357980 5 251321 71885.3 0 251321 6 138865 17971.3 0 138865 7 148822 4492.8 0 148822 8 158465 1123.2 0 158465 9 190634 280.8 0 189334 1300 10 127433 70.2 1 122111 5322 11 168478 17.6 1 162191 6287 12 199510 4.4 1 191691 7819 13 225998 4.4 1 217700 8298 14 177156 4.4 1 171162 5994 15 234584 4.4 1 226080 8504 16 198858 4.4 1 191139 7719 17 191123 4.4 1 185245 5878 18 178495 4.4 1 172778 5717 19 109217 4.4 1 105914 3303 20 156180 4.4 1 149920 6260 21 199843 4.4 1 190602 9241 22 229926 4.4 1 222565 7361 23 160663 4.4 1 155332 5331 24 189233 4.4 1 184218 5015 25 212744 4.4 1 206776 5968 26 230380 4.4 1 223336 7044 27 275391 4.4 1 268286 7105 28 115258 4.4 1 111493 3765 29 182231 4.4 1 176499 5732 30 161880 4.4 1 158009 3871 31 109720 4.4 1 106312 3408 32 196618 4.4 1 191998 4620 33 155576 4.4 1 151780 3796 34 223933 4.4 1 218073 5860 35 179085 4.4 1 175124 3961 36 382074 4.4 1 373523 8551 37 51415 4.4 1 49695 1720 38 208735 4.4 1 204373 4362 39 133891 4.4 1 130380 3511 40 141199 4.4 1 137653 3546 41 141433 4.4 1 137945 3488 42 167240 4.4 1 162717 4523 43 266848 4.4 1 259389 7459 44 151264 4.4 1 147592 3672 45 435130 4.4 1 427147 7983 46 43271 4.4 1 41260 2011 47 192372 4.4 1 188955 3417 48 175208 4.4 1 171910 3298 49 193059 4.4 1 189395 3664 50 123629 4.4 1 120578 3051 51 135572 4.4 1 132432 3140 52 121540 4.4 1 119019 2521 53 176343 4.4 1 172178 4165 54 246205 4.4 1 240342 5863 55 317966 4.4 1 311627 6339 56 185183 4.4 1 181656 3527 57 139994 4.4 1 137228 2766 58 192702 4.4 1 188942 3760 59 193828 4.4 1 190398 3430 60 137239 4.4 1 134591 2648 61 129484 4.4 1 126877 2607 62 107127 4.4 1 104790 2337 63 164918 4.4 1 161127 3791 64 193713 4.4 1 189826 3887 65 200176 4.4 1 196084 4092 66 255550 4.4 1 250630 4920 67 218060 4.4 1 213754 4306 68 234322 4.4 1 229538 4784 69 249930 4.4 1 244668 5262 70 272085 4.4 1 266604 5481 71 404097 4.4 1 396277 7820 72 4316798 4.4 1 4290132 26666 73 856365 4.4 1 848645 7720 74 186896 4.4 1 184648 2248 75 72978 4.4 1 71709 1269 76 49783 4.4 1 48614 1169 77 49628 4.4 1 48517 1111 78 40674 4.4 1 39679 995 79 36778 4.4 1 35979 799 80 30462 4.4 1 29700 762 81 27342 4.4 1 26640 702 82 25172 4.4 1 24517 655 83 27025 4.4 1 26361 664 84 30366 4.4 1 29598 768 85 35406 4.4 1 34594 812 86 36296 4.4 1 35495 801 87 36165 4.4 1 35229 936 88 35244 4.4 1 34378 866 89 32654 4.4 1 31795 859 90 26622 4.4 1 25953 669 91 21181 4.4 1 20586 595 92 18126 4.4 1 17627 499 93 18147 4.4 1 17605 542 94 20897 4.4 1 20186 711 95 26232 4.4 1 25551 681 96 31860 4.4 1 31084 776 97 32298 4.4 1 31477 821 98 30420 4.4 1 29654 766 99 27330 4.4 1 26625 705 100 24071 4.4 1 23440 631 101 20090 4.4 1 19569 521 102 26131 4.4 1 25611 520 103 15595 4.4 1 15164 431 104 15907 4.4 1 15388 519 105 20827 4.4 1 20207 620 106 26375 4.4 1 25644 731 107 29802 4.4 1 29133 669 108 27794 4.4 1 27094 700 109 23598 4.4 1 22961 637 110 20007 4.4 1 19449 558 111 15766 4.4 1 15317 449 112 12499 4.4 1 12097 402 113 10620 4.4 1 10199 421 114 12004 4.4 1 11600 404 115 15542 4.4 1 15057 485 116 18195 4.4 1 17703 492 117 17751 4.4 1 17304 447 118 15946 4.4 1 15474 472 119 12198 4.4 1 11814 384 120 9382 4.4 1 8998 384 121 8815 4.4 1 8469 346 122 8324 4.4 1 8000 324 123 7644 4.4 1 7327 317 124 6260 4.4 1 6003 257 125 1445 4.4 1 1238 207 126 557 4.4 1 350 207 127 477 4.4 1 229 248 128 347 4.4 1 129 218 129 301 4.4 1 76 225 130 290 4.4 1 70 220 131 241 4.4 1 56 185 132 316 4.4 1 72 244 133 270 4.4 1 25 245 134 202 4.4 1 12 190 135 206 4.4 1 12 194 136 208 4.4 1 14 194 137 187 4.4 1 7 180 138 260 4.4 1 4 256 139 267 4.4 1 9 258 140 196 4.4 1 7 189 141 249 4.4 1 6 243 142 449 4.4 1 26 423 143 787 4.4 1 12 775 144 168 4.4 1 3 165 145 260 4.4 1 5 255 146 117 4.4 1 1 116 147 170 4.4 1 2 168 148 432 4.4 1 4 428 149 143 4.4 1 3 140 150 92 4.4 1 0 92 151 50 4.4 1 0 50 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R1_001.fastq.gz ============================================= 73610508 sequences processed in total