SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 382246). Second best hit was Nextera (count: 1) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 442.57 s (4 us/read; 15.28 M reads/minute). === Summary === Total reads processed: 112,706,276 Reads with adapters: 78,369,527 (69.5%) Reads written (passing filters): 112,706,276 (100.0%) Total basepairs processed: 16,905,941,400 bp Quality-trimmed: 25,158,265 bp (0.1%) Total written (filtered): 14,312,572,664 bp (84.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 78369527 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.1% C: 9.8% G: 19.7% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22613071 28176569.0 0 22613071 2 2300394 7044142.2 0 2300394 3 1191481 1761035.6 0 1191481 4 736265 440258.9 0 736265 5 556744 110064.7 0 556744 6 521852 27516.2 0 521852 7 432500 6879.0 0 432500 8 542896 1719.8 0 542896 9 541192 429.9 0 533921 7271 10 495976 107.5 1 461928 34048 11 558120 26.9 1 506660 51460 12 551298 6.7 1 505922 45376 13 542939 1.7 1 497854 45085 14 564136 1.7 1 512614 51522 15 569498 1.7 1 521423 48075 16 563578 1.7 1 509820 53758 17 682231 1.7 1 615144 67087 18 558002 1.7 1 512187 45815 19 496544 1.7 1 454420 42124 20 576298 1.7 1 529271 47027 21 637299 1.7 1 580654 56645 22 542521 1.7 1 500784 41737 23 624224 1.7 1 570946 53278 24 590519 1.7 1 532912 57607 25 607047 1.7 1 556132 50915 26 572302 1.7 1 527531 44771 27 630635 1.7 1 573588 57047 28 620404 1.7 1 568899 51505 29 625305 1.7 1 567099 58206 30 664393 1.7 1 616071 48322 31 510018 1.7 1 469355 40663 32 637215 1.7 1 584852 52363 33 597607 1.7 1 545528 52079 34 753926 1.7 1 688559 65367 35 503645 1.7 1 462577 41068 36 630961 1.7 1 577612 53349 37 659262 1.7 1 604319 54943 38 595913 1.7 1 547877 48036 39 653746 1.7 1 597162 56584 40 670529 1.7 1 610664 59865 41 732564 1.7 1 667967 64597 42 545711 1.7 1 495424 50287 43 991735 1.7 1 924678 67057 44 286953 1.7 1 256328 30625 45 652219 1.7 1 601722 50497 46 619313 1.7 1 571113 48200 47 635341 1.7 1 585973 49368 48 610799 1.7 1 562441 48358 49 674495 1.7 1 617955 56540 50 598712 1.7 1 554202 44510 51 649220 1.7 1 598179 51041 52 650919 1.7 1 595866 55053 53 695670 1.7 1 642854 52816 54 545982 1.7 1 504022 41960 55 632591 1.7 1 583378 49213 56 771796 1.7 1 714466 57330 57 493419 1.7 1 450919 42500 58 643644 1.7 1 599707 43937 59 562738 1.7 1 517495 45243 60 620089 1.7 1 571985 48104 61 599005 1.7 1 554664 44341 62 665940 1.7 1 617471 48469 63 511736 1.7 1 469216 42520 64 570922 1.7 1 530032 40890 65 624134 1.7 1 576865 47269 66 644685 1.7 1 596010 48675 67 692204 1.7 1 630686 61518 68 1251198 1.7 1 1176122 75076 69 255502 1.7 1 232815 22687 70 102840 1.7 1 86533 16307 71 343135 1.7 1 318441 24694 72 484356 1.7 1 451690 32666 73 511359 1.7 1 476313 35046 74 501885 1.7 1 465645 36240 75 495613 1.7 1 458847 36766 76 482971 1.7 1 446569 36402 77 471725 1.7 1 437257 34468 78 457894 1.7 1 423781 34113 79 452070 1.7 1 418062 34008 80 438484 1.7 1 405088 33396 81 425410 1.7 1 393919 31491 82 414132 1.7 1 383041 31091 83 396751 1.7 1 367831 28920 84 386912 1.7 1 357963 28949 85 373056 1.7 1 345296 27760 86 351920 1.7 1 325697 26223 87 339788 1.7 1 315178 24610 88 331230 1.7 1 306931 24299 89 311047 1.7 1 288166 22881 90 302757 1.7 1 280581 22176 91 287473 1.7 1 266368 21105 92 274821 1.7 1 254675 20146 93 261527 1.7 1 242454 19073 94 247083 1.7 1 228486 18597 95 229569 1.7 1 212524 17045 96 215425 1.7 1 199345 16080 97 200580 1.7 1 186258 14322 98 186104 1.7 1 172508 13596 99 176938 1.7 1 163984 12954 100 163824 1.7 1 151757 12067 101 152410 1.7 1 141174 11236 102 139508 1.7 1 128964 10544 103 126668 1.7 1 117083 9585 104 114659 1.7 1 106240 8419 105 103515 1.7 1 95951 7564 106 93675 1.7 1 86344 7331 107 82801 1.7 1 76358 6443 108 74274 1.7 1 68589 5685 109 65750 1.7 1 60455 5295 110 58361 1.7 1 53718 4643 111 51503 1.7 1 47445 4058 112 46515 1.7 1 42704 3811 113 39788 1.7 1 36495 3293 114 35516 1.7 1 32502 3014 115 29286 1.7 1 26808 2478 116 25103 1.7 1 22972 2131 117 21040 1.7 1 19128 1912 118 17330 1.7 1 15763 1567 119 14917 1.7 1 13608 1309 120 12642 1.7 1 11544 1098 121 10638 1.7 1 9581 1057 122 8906 1.7 1 8053 853 123 7247 1.7 1 6562 685 124 6246 1.7 1 5598 648 125 5323 1.7 1 4772 551 126 5106 1.7 1 4581 525 127 4365 1.7 1 3924 441 128 3325 1.7 1 2922 403 129 2686 1.7 1 2381 305 130 3038 1.7 1 2747 291 131 4431 1.7 1 4079 352 132 5138 1.7 1 4758 380 133 6888 1.7 1 6396 492 134 9151 1.7 1 8614 537 135 3733 1.7 1 3470 263 136 1176 1.7 1 1019 157 137 621 1.7 1 528 93 138 473 1.7 1 413 60 139 304 1.7 1 257 47 140 204 1.7 1 168 36 141 175 1.7 1 143 32 142 95 1.7 1 74 21 143 82 1.7 1 66 16 144 113 1.7 1 89 24 145 229 1.7 1 203 26 146 212 1.7 1 174 38 147 863 1.7 1 726 137 148 473 1.7 1 383 90 149 260 1.7 1 220 40 150 2364 1.7 1 1963 401 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L002_R1_001.fastq.gz ============================================= 112706276 sequences processed in total