SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_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_7_S2_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2970.78 s (34 us/read; 1.78 M reads/minute). === Summary === Total reads processed: 88,314,076 Reads with adapters: 41,704,051 (47.2%) Reads written (passing filters): 88,314,076 (100.0%) Total basepairs processed: 13,335,425,476 bp Quality-trimmed: 243,789,443 bp (1.8%) Total written (filtered): 11,791,021,808 bp (88.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 41704051 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.8% C: 33.2% G: 23.0% T: 27.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11837322 22078519.0 0 11837322 2 3527103 5519629.8 0 3527103 3 1055780 1379907.4 0 1055780 4 460645 344976.9 0 460645 5 315456 86244.2 0 315456 6 188628 21561.1 0 188628 7 190525 5390.3 0 190525 8 207470 1347.6 0 207470 9 251241 336.9 0 249787 1454 10 167709 84.2 1 161196 6513 11 221233 21.1 1 213547 7686 12 262000 5.3 1 252369 9631 13 297890 5.3 1 287833 10057 14 230702 5.3 1 223429 7273 15 309660 5.3 1 299147 10513 16 260728 5.3 1 251292 9436 17 242656 5.3 1 235323 7333 18 237876 5.3 1 230817 7059 19 139718 5.3 1 135765 3953 20 202049 5.3 1 194615 7434 21 251904 5.3 1 241137 10767 22 303447 5.3 1 294210 9237 23 211360 5.3 1 204823 6537 24 250316 5.3 1 244006 6310 25 278768 5.3 1 271545 7223 26 299714 5.3 1 291442 8272 27 355283 5.3 1 346826 8457 28 152942 5.3 1 148316 4626 29 238366 5.3 1 231246 7120 30 210978 5.3 1 206422 4556 31 142801 5.3 1 138596 4205 32 275083 5.3 1 269385 5698 33 177507 5.3 1 173537 3970 34 230569 5.3 1 225408 5161 35 299884 5.3 1 292046 7838 36 455969 5.3 1 446019 9950 37 132116 5.3 1 128178 3938 38 359119 5.3 1 351705 7414 39 71721 5.3 1 69697 2024 40 193980 5.3 1 189437 4543 41 235364 5.3 1 229027 6337 42 239292 5.3 1 234294 4998 43 256044 5.3 1 250073 5971 44 203721 5.3 1 199825 3896 45 567194 5.3 1 558017 9177 46 49086 5.3 1 46905 2181 47 252827 5.3 1 248801 4026 48 215878 5.3 1 212344 3534 49 255712 5.3 1 251231 4481 50 154568 5.3 1 150928 3640 51 178393 5.3 1 174448 3945 52 155561 5.3 1 152621 2940 53 226654 5.3 1 221610 5044 54 320581 5.3 1 313548 7033 55 407318 5.3 1 399861 7457 56 237563 5.3 1 233312 4251 57 185492 5.3 1 182108 3384 58 248685 5.3 1 244214 4471 59 248466 5.3 1 244446 4020 60 180262 5.3 1 177007 3255 61 165164 5.3 1 162055 3109 62 139065 5.3 1 136159 2906 63 212290 5.3 1 207804 4486 64 247953 5.3 1 243312 4641 65 255639 5.3 1 250695 4944 66 327156 5.3 1 321087 6069 67 281328 5.3 1 276128 5200 68 302626 5.3 1 296931 5695 69 317025 5.3 1 310666 6359 70 344575 5.3 1 337918 6657 71 503276 5.3 1 493996 9280 72 5408619 5.3 1 5377829 30790 73 1069104 5.3 1 1060010 9094 74 235268 5.3 1 232645 2623 75 94504 5.3 1 92878 1626 76 63361 5.3 1 62005 1356 77 64135 5.3 1 62847 1288 78 52148 5.3 1 50985 1163 79 47636 5.3 1 46650 986 80 40296 5.3 1 39394 902 81 35402 5.3 1 34516 886 82 31834 5.3 1 31074 760 83 34390 5.3 1 33526 864 84 39046 5.3 1 38168 878 85 45220 5.3 1 44310 910 86 45545 5.3 1 44554 991 87 45136 5.3 1 44123 1013 88 44261 5.3 1 43299 962 89 40216 5.3 1 39310 906 90 33495 5.3 1 32741 754 91 26435 5.3 1 25779 656 92 22863 5.3 1 22247 616 93 22930 5.3 1 22312 618 94 26357 5.3 1 25697 660 95 32797 5.3 1 31989 808 96 39714 5.3 1 38882 832 97 40006 5.3 1 39125 881 98 37463 5.3 1 36628 835 99 34380 5.3 1 33603 777 100 29953 5.3 1 29256 697 101 26228 5.3 1 25604 624 102 39583 5.3 1 39031 552 103 20525 5.3 1 20047 478 104 19605 5.3 1 19099 506 105 25882 5.3 1 25264 618 106 32778 5.3 1 31934 844 107 36206 5.3 1 35451 755 108 33501 5.3 1 32769 732 109 28532 5.3 1 27840 692 110 24453 5.3 1 23875 578 111 19581 5.3 1 19097 484 112 15397 5.3 1 14913 484 113 13215 5.3 1 12779 436 114 14860 5.3 1 14402 458 115 19757 5.3 1 19247 510 116 22791 5.3 1 22282 509 117 21938 5.3 1 21393 545 118 19251 5.3 1 18784 467 119 15093 5.3 1 14669 424 120 11635 5.3 1 11263 372 121 10520 5.3 1 10184 336 122 10224 5.3 1 9899 325 123 9571 5.3 1 9177 394 124 7735 5.3 1 7443 292 125 1642 5.3 1 1443 199 126 596 5.3 1 359 237 127 551 5.3 1 294 257 128 367 5.3 1 152 215 129 326 5.3 1 102 224 130 354 5.3 1 88 266 131 295 5.3 1 64 231 132 327 5.3 1 69 258 133 260 5.3 1 24 236 134 215 5.3 1 15 200 135 244 5.3 1 14 230 136 243 5.3 1 7 236 137 220 5.3 1 18 202 138 305 5.3 1 5 300 139 307 5.3 1 5 302 140 231 5.3 1 9 222 141 302 5.3 1 7 295 142 436 5.3 1 26 410 143 871 5.3 1 15 856 144 219 5.3 1 3 216 145 283 5.3 1 3 280 146 109 5.3 1 0 109 147 169 5.3 1 0 169 148 485 5.3 1 5 480 149 184 5.3 1 0 184 150 98 5.3 1 1 97 151 61 5.3 1 1 60 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R1_001.fastq.gz ============================================= 88314076 sequences processed in total