SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_L002_R2_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: 417809). Second best hit was Nextera (count: 0) 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_F2_S22_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 353.56 s (4 us/read; 13.86 M reads/minute). === Summary === Total reads processed: 81,699,034 Reads with adapters: 57,979,113 (71.0%) Reads written (passing filters): 81,699,034 (100.0%) Total basepairs processed: 12,254,855,100 bp Quality-trimmed: 41,067,962 bp (0.3%) Total written (filtered): 10,294,963,583 bp (84.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57979113 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.7% C: 9.9% G: 22.0% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15214651 20424758.5 0 15214651 2 1629144 5106189.6 0 1629144 3 914799 1276547.4 0 914799 4 558975 319136.9 0 558975 5 482109 79784.2 0 482109 6 418136 19946.1 0 418136 7 337570 4986.5 0 337570 8 479586 1246.6 0 479586 9 390650 311.7 0 389615 1035 10 405041 77.9 1 379605 25436 11 435020 19.5 1 401922 33098 12 439217 4.9 1 406727 32490 13 510754 1.2 1 472376 38378 14 448612 1.2 1 412140 36472 15 384027 1.2 1 355388 28639 16 544298 1.2 1 502865 41433 17 437427 1.2 1 403719 33708 18 402979 1.2 1 373023 29956 19 503067 1.2 1 466488 36579 20 474971 1.2 1 440326 34645 21 421874 1.2 1 390910 30964 22 467522 1.2 1 433687 33835 23 490952 1.2 1 454530 36422 24 482710 1.2 1 447678 35032 25 536922 1.2 1 501311 35611 26 451785 1.2 1 415820 35965 27 506974 1.2 1 466123 40851 28 440254 1.2 1 412940 27314 29 498335 1.2 1 462544 35791 30 447616 1.2 1 418293 29323 31 531574 1.2 1 494290 37284 32 441801 1.2 1 413285 28516 33 515665 1.2 1 478090 37575 34 666212 1.2 1 619804 46408 35 346551 1.2 1 323116 23435 36 489499 1.2 1 454133 35366 37 532182 1.2 1 495525 36657 38 478707 1.2 1 449260 29447 39 471359 1.2 1 443454 27905 40 529670 1.2 1 494697 34973 41 516177 1.2 1 483272 32905 42 520597 1.2 1 487926 32671 43 474470 1.2 1 444318 30152 44 553215 1.2 1 517017 36198 45 566191 1.2 1 530084 36107 46 413041 1.2 1 386808 26233 47 502147 1.2 1 473043 29104 48 484308 1.2 1 456231 28077 49 510392 1.2 1 478462 31930 50 506166 1.2 1 473768 32398 51 605207 1.2 1 567914 37293 52 440187 1.2 1 413511 26676 53 531819 1.2 1 501544 30275 54 389426 1.2 1 367011 22415 55 491938 1.2 1 464562 27376 56 495033 1.2 1 464600 30433 57 481452 1.2 1 455340 26112 58 468033 1.2 1 442245 25788 59 468551 1.2 1 441634 26917 60 478522 1.2 1 450900 27622 61 487423 1.2 1 460617 26806 62 522057 1.2 1 491364 30693 63 673446 1.2 1 638844 34602 64 507915 1.2 1 484583 23332 65 350472 1.2 1 331804 18668 66 389451 1.2 1 368357 21094 67 396849 1.2 1 374262 22587 68 394541 1.2 1 372684 21857 69 391045 1.2 1 368794 22251 70 390887 1.2 1 368825 22062 71 401886 1.2 1 379624 22262 72 392080 1.2 1 370490 21590 73 411065 1.2 1 388688 22377 74 374532 1.2 1 353760 20772 75 357961 1.2 1 338145 19816 76 346375 1.2 1 327002 19373 77 331945 1.2 1 313179 18766 78 321538 1.2 1 303798 17740 79 313177 1.2 1 295979 17198 80 304441 1.2 1 287925 16516 81 293724 1.2 1 277950 15774 82 282766 1.2 1 267333 15433 83 270058 1.2 1 255507 14551 84 265196 1.2 1 251091 14105 85 257861 1.2 1 244467 13394 86 250545 1.2 1 237466 13079 87 251526 1.2 1 238890 12636 88 240557 1.2 1 228280 12277 89 211890 1.2 1 200619 11271 90 199074 1.2 1 188762 10312 91 188118 1.2 1 178454 9664 92 176434 1.2 1 167450 8984 93 173462 1.2 1 164594 8868 94 163597 1.2 1 155286 8311 95 151070 1.2 1 143169 7901 96 142096 1.2 1 134776 7320 97 132469 1.2 1 125885 6584 98 123111 1.2 1 116966 6145 99 116382 1.2 1 110385 5997 100 108683 1.2 1 103116 5567 101 96750 1.2 1 91809 4941 102 88826 1.2 1 84306 4520 103 81399 1.2 1 77208 4191 104 76198 1.2 1 72290 3908 105 68158 1.2 1 64724 3434 106 61130 1.2 1 58100 3030 107 52011 1.2 1 49328 2683 108 45529 1.2 1 43239 2290 109 41683 1.2 1 39576 2107 110 36218 1.2 1 34303 1915 111 32883 1.2 1 31247 1636 112 29793 1.2 1 28318 1475 113 24999 1.2 1 23719 1280 114 22662 1.2 1 21525 1137 115 18096 1.2 1 17176 920 116 15270 1.2 1 14496 774 117 12170 1.2 1 11514 656 118 10414 1.2 1 9832 582 119 8403 1.2 1 7959 444 120 7343 1.2 1 6952 391 121 6317 1.2 1 5964 353 122 5204 1.2 1 4941 263 123 4340 1.2 1 4122 218 124 3564 1.2 1 3376 188 125 2965 1.2 1 2783 182 126 2377 1.2 1 2237 140 127 1922 1.2 1 1812 110 128 1530 1.2 1 1436 94 129 1224 1.2 1 1157 67 130 1037 1.2 1 967 70 131 861 1.2 1 806 55 132 686 1.2 1 633 53 133 661 1.2 1 620 41 134 651 1.2 1 603 48 135 432 1.2 1 408 24 136 309 1.2 1 286 23 137 192 1.2 1 170 22 138 168 1.2 1 155 13 139 128 1.2 1 109 19 140 85 1.2 1 78 7 141 53 1.2 1 46 7 142 58 1.2 1 51 7 143 31 1.2 1 26 5 144 40 1.2 1 32 8 145 40 1.2 1 33 7 146 40 1.2 1 29 11 147 75 1.2 1 67 8 148 58 1.2 1 52 6 149 37 1.2 1 34 3 150 319 1.2 1 294 25 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_L002_R2_001.fastq.gz ============================================= 81699034 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 81699034 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 345792 (0.42%)