SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_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: 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_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 331.66 s (4 us/read; 14.78 M reads/minute). === Summary === Total reads processed: 81,699,034 Reads with adapters: 58,422,606 (71.5%) Reads written (passing filters): 81,699,034 (100.0%) Total basepairs processed: 12,254,855,100 bp Quality-trimmed: 19,487,828 bp (0.2%) Total written (filtered): 10,283,682,296 bp (83.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58422606 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.4% C: 11.4% G: 19.4% T: 33.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15199129 20424758.5 0 15199129 2 1580922 5106189.6 0 1580922 3 842043 1276547.4 0 842043 4 550022 319136.9 0 550022 5 449997 79784.2 0 449997 6 434481 19946.1 0 434481 7 347898 4986.5 0 347898 8 441084 1246.6 0 441084 9 443045 311.7 0 438482 4563 10 405413 77.9 1 382098 23315 11 450388 19.5 1 415672 34716 12 442770 4.9 1 412586 30184 13 446024 1.2 1 415108 30916 14 453376 1.2 1 419388 33988 15 468278 1.2 1 435263 33015 16 452666 1.2 1 416929 35737 17 549238 1.2 1 503600 45638 18 466886 1.2 1 435945 30941 19 393788 1.2 1 366567 27221 20 467902 1.2 1 436166 31736 21 521792 1.2 1 483620 38172 22 433680 1.2 1 406255 27425 23 504819 1.2 1 468719 36100 24 475517 1.2 1 437053 38464 25 491820 1.2 1 457067 34753 26 461178 1.2 1 431235 29943 27 512653 1.2 1 473769 38884 28 491651 1.2 1 457681 33970 29 512510 1.2 1 470963 41547 30 548141 1.2 1 514010 34131 31 409025 1.2 1 380832 28193 32 540631 1.2 1 502491 38140 33 452892 1.2 1 421055 31837 34 512380 1.2 1 471655 40725 35 569764 1.2 1 523370 46394 36 519856 1.2 1 484148 35708 37 553142 1.2 1 519802 33340 38 400544 1.2 1 364810 35734 39 573002 1.2 1 528499 44503 40 466836 1.2 1 435154 31682 41 600726 1.2 1 554364 46362 42 453939 1.2 1 416218 37721 43 790864 1.2 1 744421 46443 44 241028 1.2 1 218439 22589 45 522905 1.2 1 486598 36307 46 536313 1.2 1 498381 37932 47 536772 1.2 1 501509 35263 48 445960 1.2 1 412336 33624 49 569976 1.2 1 527084 42892 50 451713 1.2 1 423569 28144 51 503554 1.2 1 469351 34203 52 559241 1.2 1 515373 43868 53 626961 1.2 1 588950 38011 54 397202 1.2 1 368180 29022 55 510273 1.2 1 477059 33214 56 566018 1.2 1 530313 35705 57 490065 1.2 1 455879 34186 58 448852 1.2 1 423488 25364 59 352650 1.2 1 326693 25957 60 521343 1.2 1 488341 33002 61 489445 1.2 1 459888 29557 62 454351 1.2 1 425498 28853 63 442859 1.2 1 412719 30140 64 413454 1.2 1 388538 24916 65 428487 1.2 1 400331 28156 66 475641 1.2 1 444595 31046 67 527546 1.2 1 487484 40062 68 932793 1.2 1 883259 49534 69 306211 1.2 1 285490 20721 70 98330 1.2 1 86452 11878 71 183213 1.2 1 170097 13116 72 347828 1.2 1 327310 20518 73 384493 1.2 1 361546 22947 74 375434 1.2 1 351755 23679 75 372810 1.2 1 349151 23659 76 366345 1.2 1 341732 24613 77 349631 1.2 1 326987 22644 78 336085 1.2 1 313727 22358 79 334791 1.2 1 312735 22056 80 320766 1.2 1 299322 21444 81 308813 1.2 1 288662 20151 82 303376 1.2 1 282871 20505 83 287613 1.2 1 268884 18729 84 281524 1.2 1 262646 18878 85 269523 1.2 1 251601 17922 86 255982 1.2 1 238963 17019 87 246467 1.2 1 230371 16096 88 240096 1.2 1 224172 15924 89 222064 1.2 1 207380 14684 90 214626 1.2 1 200391 14235 91 204511 1.2 1 191212 13299 92 193574 1.2 1 180679 12895 93 185417 1.2 1 173008 12409 94 174914 1.2 1 163234 11680 95 159670 1.2 1 148732 10938 96 150695 1.2 1 140365 10330 97 140751 1.2 1 131592 9159 98 129553 1.2 1 120450 9103 99 122439 1.2 1 114105 8334 100 113910 1.2 1 106001 7909 101 103551 1.2 1 96319 7232 102 95288 1.2 1 88666 6622 103 86137 1.2 1 80145 5992 104 77327 1.2 1 71858 5469 105 69993 1.2 1 65045 4948 106 63171 1.2 1 58489 4682 107 54679 1.2 1 50722 3957 108 49406 1.2 1 45775 3631 109 44550 1.2 1 41176 3374 110 38825 1.2 1 35771 3054 111 33501 1.2 1 30848 2653 112 30928 1.2 1 28428 2500 113 25660 1.2 1 23574 2086 114 23733 1.2 1 21729 2004 115 19374 1.2 1 17711 1663 116 16667 1.2 1 15185 1482 117 13526 1.2 1 12278 1248 118 11411 1.2 1 10398 1013 119 9123 1.2 1 8243 880 120 8085 1.2 1 7320 765 121 6821 1.2 1 6153 668 122 5630 1.2 1 5011 619 123 4598 1.2 1 4108 490 124 3796 1.2 1 3390 406 125 3140 1.2 1 2802 338 126 2509 1.2 1 2205 304 127 2125 1.2 1 1865 260 128 1671 1.2 1 1452 219 129 1329 1.2 1 1142 187 130 1120 1.2 1 991 129 131 940 1.2 1 808 132 132 761 1.2 1 666 95 133 675 1.2 1 585 90 134 682 1.2 1 604 78 135 447 1.2 1 388 59 136 330 1.2 1 286 44 137 223 1.2 1 175 48 138 187 1.2 1 160 27 139 149 1.2 1 117 32 140 100 1.2 1 80 20 141 64 1.2 1 50 14 142 63 1.2 1 51 12 143 43 1.2 1 29 14 144 41 1.2 1 32 9 145 44 1.2 1 36 8 146 35 1.2 1 24 11 147 75 1.2 1 69 6 148 65 1.2 1 52 13 149 34 1.2 1 28 6 150 405 1.2 1 345 60 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_L002_R1_001.fastq.gz ============================================= 81699034 sequences processed in total