SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L002_R2_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 5357.16 s (48 us/read; 1.26 M reads/minute). === Summary === Total reads processed: 112,706,276 Reads with adapters: 78,702,417 (69.8%) Reads written (passing filters): 112,706,276 (100.0%) Total basepairs processed: 16,905,941,400 bp Quality-trimmed: 71,979,281 bp (0.4%) Total written (filtered): 14,323,556,948 bp (84.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 78702417 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.2% C: 9.3% G: 21.4% T: 32.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24049259 28176569.0 0 24049259 2 2103822 7044142.2 0 2103822 3 1234623 1761035.6 0 1234623 4 713926 440258.9 0 713926 5 593548 110064.7 0 593548 6 520489 27516.2 0 520489 7 412592 6879.0 0 412592 8 591207 1719.8 0 591207 9 484607 429.9 0 482791 1816 10 495729 107.5 1 462070 33659 11 538210 26.9 1 494011 44199 12 541780 6.7 1 498135 43645 13 624482 1.7 1 573035 51447 14 557547 1.7 1 507941 49606 15 471226 1.7 1 432359 38867 16 663767 1.7 1 609668 54099 17 541007 1.7 1 495593 45414 18 492493 1.7 1 452345 40148 19 620390 1.7 1 571312 49078 20 584573 1.7 1 538235 46338 21 515948 1.7 1 474451 41497 22 574265 1.7 1 529265 45000 23 609172 1.7 1 559895 49277 24 593165 1.7 1 546488 46677 25 658890 1.7 1 611466 47424 26 563159 1.7 1 515387 47772 27 631617 1.7 1 576879 54738 28 542598 1.7 1 506943 35655 29 609830 1.7 1 564437 45393 30 560210 1.7 1 522268 37942 31 641241 1.7 1 594510 46731 32 544093 1.7 1 508074 36019 33 636374 1.7 1 588179 48195 34 815281 1.7 1 756328 58953 35 430454 1.7 1 399829 30625 36 615273 1.7 1 568703 46570 37 652049 1.7 1 605036 47013 38 597268 1.7 1 559355 37913 39 577372 1.7 1 541971 35401 40 649729 1.7 1 605597 44132 41 640639 1.7 1 597788 42851 42 636924 1.7 1 595731 41193 43 595156 1.7 1 555850 39306 44 689081 1.7 1 641836 47245 45 705414 1.7 1 658767 46647 46 511671 1.7 1 477756 33915 47 627959 1.7 1 589895 38064 48 606191 1.7 1 569490 36701 49 638780 1.7 1 597375 41405 50 632872 1.7 1 591113 41759 51 767529 1.7 1 718431 49098 52 550691 1.7 1 515808 34883 53 670844 1.7 1 631272 39572 54 486646 1.7 1 457582 29064 55 619044 1.7 1 583828 35216 56 629194 1.7 1 589212 39982 57 612138 1.7 1 577341 34797 58 592465 1.7 1 558875 33590 59 595468 1.7 1 560221 35247 60 612569 1.7 1 576229 36340 61 622280 1.7 1 586602 35678 62 676352 1.7 1 634848 41504 63 865976 1.7 1 819740 46236 64 686055 1.7 1 654087 31968 65 461983 1.7 1 436125 25858 66 506619 1.7 1 477735 28884 67 507018 1.7 1 477302 29716 68 510556 1.7 1 481168 29388 69 507332 1.7 1 477239 30093 70 512308 1.7 1 482423 29885 71 532127 1.7 1 501527 30600 72 518080 1.7 1 487908 30172 73 537157 1.7 1 506806 30351 74 495539 1.7 1 466890 28649 75 470503 1.7 1 443438 27065 76 452980 1.7 1 426860 26120 77 443451 1.7 1 417656 25795 78 435086 1.7 1 409995 25091 79 419597 1.7 1 395575 24022 80 414921 1.7 1 392020 22901 81 399796 1.7 1 377201 22595 82 383327 1.7 1 361982 21345 83 367682 1.7 1 347411 20271 84 357304 1.7 1 337566 19738 85 348720 1.7 1 329480 19240 86 342051 1.7 1 323486 18565 87 342842 1.7 1 324860 17982 88 330713 1.7 1 313318 17395 89 294825 1.7 1 279096 15729 90 280371 1.7 1 265521 14850 91 263612 1.7 1 249496 14116 92 248322 1.7 1 235160 13162 93 241085 1.7 1 228414 12671 94 227365 1.7 1 215260 12105 95 212715 1.7 1 201138 11577 96 201763 1.7 1 191081 10682 97 190347 1.7 1 180592 9755 98 180927 1.7 1 171879 9048 99 177126 1.7 1 168081 9045 100 161967 1.7 1 153628 8339 101 143338 1.7 1 136043 7295 102 127435 1.7 1 120719 6716 103 114642 1.7 1 108603 6039 104 106928 1.7 1 101222 5706 105 97130 1.7 1 92087 5043 106 88346 1.7 1 83845 4501 107 77435 1.7 1 73389 4046 108 67272 1.7 1 63761 3511 109 60831 1.7 1 57633 3198 110 53937 1.7 1 51056 2881 111 49603 1.7 1 47000 2603 112 44226 1.7 1 41868 2358 113 38028 1.7 1 35980 2048 114 33519 1.7 1 31680 1839 115 26723 1.7 1 25283 1440 116 22936 1.7 1 21626 1310 117 19039 1.7 1 17966 1073 118 15805 1.7 1 14850 955 119 13430 1.7 1 12634 796 120 11390 1.7 1 10687 703 121 9723 1.7 1 9101 622 122 8226 1.7 1 7693 533 123 6741 1.7 1 6334 407 124 5699 1.7 1 5276 423 125 5010 1.7 1 4637 373 126 4661 1.7 1 4329 332 127 3987 1.7 1 3713 274 128 2901 1.7 1 2665 236 129 2466 1.7 1 2254 212 130 2939 1.7 1 2734 205 131 4275 1.7 1 4050 225 132 4899 1.7 1 4690 209 133 7071 1.7 1 6772 299 134 8958 1.7 1 8601 357 135 3598 1.7 1 3428 170 136 1085 1.7 1 1002 83 137 586 1.7 1 522 64 138 435 1.7 1 381 54 139 265 1.7 1 235 30 140 195 1.7 1 157 38 141 157 1.7 1 136 21 142 96 1.7 1 75 21 143 89 1.7 1 70 19 144 116 1.7 1 91 25 145 262 1.7 1 239 23 146 193 1.7 1 171 22 147 646 1.7 1 552 94 148 333 1.7 1 271 62 149 178 1.7 1 147 31 150 1314 1.7 1 1144 170 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/Sealice_F1_S20_L002_R2_001.fastq.gz ============================================= 112706276 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 159281 (0.1%)