SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L001_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: 386206). Second best hit was smallRNA (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_F1_S20_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 478.03 s (4 us/read; 14.24 M reads/minute). === Summary === Total reads processed: 113,474,961 Reads with adapters: 79,235,271 (69.8%) Reads written (passing filters): 113,474,961 (100.0%) Total basepairs processed: 17,021,244,150 bp Quality-trimmed: 73,052,751 bp (0.4%) Total written (filtered): 14,433,737,028 bp (84.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 79235271 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.2% C: 9.2% G: 21.3% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24292490 28368740.2 0 24292490 2 2172289 7092185.1 0 2172289 3 1212765 1773046.3 0 1212765 4 728934 443261.6 0 728934 5 615953 110815.4 0 615953 6 518496 27703.8 0 518496 7 424176 6926.0 0 424176 8 595932 1731.5 0 595932 9 493164 432.9 0 491188 1976 10 515557 108.2 1 490642 24915 11 544480 27.1 1 510284 34196 12 557302 6.8 1 522559 34743 13 624852 1.7 1 586293 38559 14 566086 1.7 1 527536 38550 15 479671 1.7 1 447634 32037 16 677197 1.7 1 634485 42712 17 518178 1.7 1 482968 35210 18 513709 1.7 1 481055 32654 19 623697 1.7 1 583105 40592 20 590778 1.7 1 553837 36941 21 523012 1.7 1 489156 33856 22 582166 1.7 1 546634 35532 23 607194 1.7 1 567433 39761 24 596018 1.7 1 558835 37183 25 658603 1.7 1 618497 40106 26 563795 1.7 1 525767 38028 27 625280 1.7 1 580031 45249 28 565755 1.7 1 537011 28744 29 604057 1.7 1 566572 37485 30 575342 1.7 1 545309 30033 31 637117 1.7 1 598679 38438 32 567491 1.7 1 538376 29115 33 633139 1.7 1 594872 38267 34 807925 1.7 1 759853 48072 35 450122 1.7 1 426055 24067 36 611610 1.7 1 574682 36928 37 655880 1.7 1 616910 38970 38 600986 1.7 1 571449 29537 39 595629 1.7 1 565252 30377 40 651655 1.7 1 614241 37414 41 634336 1.7 1 600514 33822 42 641088 1.7 1 607660 33428 43 603840 1.7 1 570768 33072 44 681587 1.7 1 644069 37518 45 707281 1.7 1 670903 36378 46 517703 1.7 1 489820 27883 47 633055 1.7 1 601375 31680 48 613751 1.7 1 584361 29390 49 644336 1.7 1 611009 33327 50 626710 1.7 1 592951 33759 51 770564 1.7 1 731245 39319 52 552184 1.7 1 525737 26447 53 655644 1.7 1 624724 30920 54 497055 1.7 1 473150 23905 55 622404 1.7 1 594084 28320 56 630771 1.7 1 599636 31135 57 608401 1.7 1 579359 29042 58 589791 1.7 1 563588 26203 59 602895 1.7 1 574430 28465 60 610621 1.7 1 581075 29546 61 631221 1.7 1 600250 30971 62 678983 1.7 1 645436 33547 63 884166 1.7 1 845237 38929 64 697534 1.7 1 670069 27465 65 461327 1.7 1 440187 21140 66 505461 1.7 1 482444 23017 67 504336 1.7 1 480520 23816 68 506997 1.7 1 484099 22898 69 501262 1.7 1 477906 23356 70 506318 1.7 1 482633 23685 71 530040 1.7 1 506417 23623 72 512724 1.7 1 488940 23784 73 535324 1.7 1 511542 23782 74 491314 1.7 1 470184 21130 75 468392 1.7 1 447958 20434 76 453588 1.7 1 433629 19959 77 443997 1.7 1 423454 20543 78 435469 1.7 1 416134 19335 79 419163 1.7 1 400603 18560 80 414024 1.7 1 395828 18196 81 398372 1.7 1 381040 17332 82 382299 1.7 1 365451 16848 83 366779 1.7 1 350673 16106 84 355643 1.7 1 339567 16076 85 348592 1.7 1 332671 15921 86 340981 1.7 1 325646 15335 87 343724 1.7 1 328719 15005 88 328419 1.7 1 314072 14347 89 293572 1.7 1 280847 12725 90 277907 1.7 1 265475 12432 91 261801 1.7 1 250188 11613 92 247933 1.7 1 237089 10844 93 241002 1.7 1 230436 10566 94 225907 1.7 1 216109 9798 95 212543 1.7 1 203112 9431 96 199922 1.7 1 191511 8411 97 189942 1.7 1 181742 8200 98 181068 1.7 1 173356 7712 99 177800 1.7 1 170721 7079 100 161532 1.7 1 154936 6596 101 142590 1.7 1 136815 5775 102 127109 1.7 1 121824 5285 103 114820 1.7 1 109872 4948 104 106755 1.7 1 102353 4402 105 97032 1.7 1 93102 3930 106 87939 1.7 1 84311 3628 107 77043 1.7 1 73799 3244 108 66878 1.7 1 63922 2956 109 60697 1.7 1 58149 2548 110 53817 1.7 1 51530 2287 111 49656 1.7 1 47564 2092 112 44212 1.7 1 42328 1884 113 37568 1.7 1 35930 1638 114 33504 1.7 1 32034 1470 115 26873 1.7 1 25557 1316 116 23021 1.7 1 21918 1103 117 18702 1.7 1 17804 898 118 15710 1.7 1 14954 756 119 13467 1.7 1 12827 640 120 11166 1.7 1 10610 556 121 9578 1.7 1 9044 534 122 7970 1.7 1 7515 455 123 6749 1.7 1 6389 360 124 5790 1.7 1 5438 352 125 4982 1.7 1 4674 308 126 4691 1.7 1 4415 276 127 3926 1.7 1 3689 237 128 2937 1.7 1 2717 220 129 2589 1.7 1 2397 192 130 2951 1.7 1 2762 189 131 4241 1.7 1 4050 191 132 4816 1.7 1 4604 212 133 7287 1.7 1 6984 303 134 8892 1.7 1 8589 303 135 3540 1.7 1 3386 154 136 1144 1.7 1 1071 73 137 598 1.7 1 565 33 138 406 1.7 1 369 37 139 302 1.7 1 277 25 140 227 1.7 1 197 30 141 147 1.7 1 128 19 142 76 1.7 1 62 14 143 79 1.7 1 62 17 144 94 1.7 1 81 13 145 260 1.7 1 229 31 146 164 1.7 1 145 19 147 597 1.7 1 528 69 148 305 1.7 1 255 50 149 176 1.7 1 150 26 150 1321 1.7 1 1192 129 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L001_R2_001.fastq.gz ============================================= 113474961 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 113474961 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 643628 (0.57%)