SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L001_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: 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_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 476.93 s (4 us/read; 14.28 M reads/minute). === Summary === Total reads processed: 113,474,961 Reads with adapters: 78,847,369 (69.5%) Reads written (passing filters): 113,474,961 (100.0%) Total basepairs processed: 17,021,244,150 bp Quality-trimmed: 22,715,789 bp (0.1%) Total written (filtered): 14,426,732,983 bp (84.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 78847369 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.1% C: 9.7% G: 19.7% T: 34.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22838934 28368740.2 0 22838934 2 2342589 7092185.1 0 2342589 3 1202279 1773046.3 0 1202279 4 750593 443261.6 0 750593 5 559528 110815.4 0 559528 6 524826 27703.8 0 524826 7 449332 6926.0 0 449332 8 548899 1731.5 0 548899 9 548856 432.9 0 541308 7548 10 508456 108.2 1 478983 29473 11 562956 27.1 1 517668 45288 12 559587 6.8 1 520090 39497 13 547304 1.7 1 508519 38785 14 570426 1.7 1 525734 44692 15 575858 1.7 1 534867 40991 16 569860 1.7 1 523134 46726 17 678914 1.7 1 621846 57068 18 565739 1.7 1 526451 39288 19 504906 1.7 1 468246 36660 20 580103 1.7 1 539012 41091 21 633303 1.7 1 584154 49149 22 551495 1.7 1 516023 35472 23 623244 1.7 1 577696 45548 24 597040 1.7 1 545080 51960 25 610942 1.7 1 565949 44993 26 578327 1.7 1 539305 39022 27 631060 1.7 1 581266 49794 28 620380 1.7 1 573987 46393 29 630417 1.7 1 577901 52516 30 665372 1.7 1 624016 41356 31 521479 1.7 1 485824 35655 32 637552 1.7 1 593972 43580 33 605503 1.7 1 560522 44981 34 753213 1.7 1 699064 54149 35 512573 1.7 1 477265 35308 36 633868 1.7 1 587959 45909 37 659372 1.7 1 612861 46511 38 603868 1.7 1 563307 40561 39 656560 1.7 1 609454 47106 40 670911 1.7 1 620635 50276 41 733444 1.7 1 678908 54536 42 554355 1.7 1 510902 43453 43 1004589 1.7 1 949034 55555 44 281497 1.7 1 254795 26702 45 650424 1.7 1 607820 42604 46 622059 1.7 1 580617 41442 47 641812 1.7 1 599651 42161 48 616364 1.7 1 574406 41958 49 673245 1.7 1 623804 49441 50 604428 1.7 1 565417 39011 51 645021 1.7 1 600411 44610 52 648661 1.7 1 600394 48267 53 693327 1.7 1 647436 45891 54 550715 1.7 1 514274 36441 55 631316 1.7 1 588270 43046 56 767345 1.7 1 719044 48301 57 493710 1.7 1 456524 37186 58 647241 1.7 1 610352 36889 59 560612 1.7 1 522206 38406 60 620281 1.7 1 578774 41507 61 603855 1.7 1 565232 38623 62 664795 1.7 1 623425 41370 63 508452 1.7 1 471688 36764 64 573553 1.7 1 538426 35127 65 625525 1.7 1 584793 40732 66 654791 1.7 1 611542 43249 67 693655 1.7 1 637398 56257 68 1295847 1.7 1 1228868 66979 69 207198 1.7 1 188952 18246 70 83872 1.7 1 69823 14049 71 351217 1.7 1 328576 22641 72 486564 1.7 1 456539 30025 73 511552 1.7 1 479835 31717 74 500225 1.7 1 468801 31424 75 493734 1.7 1 462637 31097 76 485479 1.7 1 455415 30064 77 472130 1.7 1 442425 29705 78 457249 1.7 1 427856 29393 79 452598 1.7 1 423758 28840 80 436888 1.7 1 409466 27422 81 424029 1.7 1 397325 26704 82 413331 1.7 1 387262 26069 83 395648 1.7 1 370721 24927 84 386472 1.7 1 362163 24309 85 373564 1.7 1 350510 23054 86 350177 1.7 1 327542 22635 87 338817 1.7 1 317459 21358 88 329564 1.7 1 308892 20672 89 310326 1.7 1 290522 19804 90 302165 1.7 1 282977 19188 91 286619 1.7 1 268441 18178 92 275091 1.7 1 257788 17303 93 261850 1.7 1 245237 16613 94 246459 1.7 1 230780 15679 95 229270 1.7 1 214573 14697 96 213682 1.7 1 200015 13667 97 200167 1.7 1 187352 12815 98 186673 1.7 1 174782 11891 99 177389 1.7 1 165973 11416 100 164170 1.7 1 153549 10621 101 152020 1.7 1 142083 9937 102 138827 1.7 1 129592 9235 103 126885 1.7 1 118589 8296 104 114180 1.7 1 106471 7709 105 103407 1.7 1 96323 7084 106 93053 1.7 1 86648 6405 107 82305 1.7 1 76807 5498 108 73960 1.7 1 68774 5186 109 66073 1.7 1 61323 4750 110 58316 1.7 1 54124 4192 111 51210 1.7 1 47563 3647 112 46457 1.7 1 43051 3406 113 39166 1.7 1 36179 2987 114 35653 1.7 1 32939 2714 115 29363 1.7 1 27078 2285 116 25352 1.7 1 23356 1996 117 20912 1.7 1 19235 1677 118 17421 1.7 1 15974 1447 119 14864 1.7 1 13576 1288 120 12650 1.7 1 11578 1072 121 10471 1.7 1 9498 973 122 8802 1.7 1 7972 830 123 7467 1.7 1 6769 698 124 6267 1.7 1 5666 601 125 5296 1.7 1 4740 556 126 5081 1.7 1 4533 548 127 4350 1.7 1 3958 392 128 3255 1.7 1 2949 306 129 2684 1.7 1 2428 256 130 3108 1.7 1 2815 293 131 4344 1.7 1 4012 332 132 4969 1.7 1 4639 330 133 7178 1.7 1 6729 449 134 9066 1.7 1 8514 552 135 3718 1.7 1 3456 262 136 1190 1.7 1 1067 123 137 629 1.7 1 542 87 138 481 1.7 1 425 56 139 351 1.7 1 310 41 140 237 1.7 1 196 41 141 164 1.7 1 133 31 142 89 1.7 1 63 26 143 91 1.7 1 63 28 144 96 1.7 1 72 24 145 237 1.7 1 190 47 146 222 1.7 1 196 26 147 852 1.7 1 739 113 148 478 1.7 1 374 104 149 260 1.7 1 214 46 150 2350 1.7 1 1965 385 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F1_S20_L001_R1_001.fastq.gz ============================================= 113474961 sequences processed in total