SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_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: 419839). 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_F2_S22_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 331.82 s (4 us/read; 14.86 M reads/minute). === Summary === Total reads processed: 82,177,525 Reads with adapters: 58,714,265 (71.4%) Reads written (passing filters): 82,177,525 (100.0%) Total basepairs processed: 12,326,628,750 bp Quality-trimmed: 17,863,332 bp (0.1%) Total written (filtered): 10,356,260,345 bp (84.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58714265 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.4% C: 11.4% G: 19.3% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15334703 20544381.2 0 15334703 2 1608191 5136095.3 0 1608191 3 847327 1284023.8 0 847327 4 558993 321006.0 0 558993 5 451836 80251.5 0 451836 6 436528 20062.9 0 436528 7 362332 5015.7 0 362332 8 445624 1253.9 0 445624 9 448853 313.5 0 444071 4782 10 414974 78.4 1 395643 19331 11 451608 19.6 1 421964 29644 12 446668 4.9 1 421394 25274 13 448758 1.2 1 423173 25585 14 458328 1.2 1 429437 28891 15 470816 1.2 1 443807 27009 16 459713 1.2 1 429546 30167 17 546940 1.2 1 508999 37941 18 471227 1.2 1 445754 25473 19 402058 1.2 1 378920 23138 20 471685 1.2 1 445002 26683 21 519729 1.2 1 487230 32499 22 441834 1.2 1 419209 22625 23 505202 1.2 1 475325 29877 24 480556 1.2 1 445808 34748 25 495463 1.2 1 465784 29679 26 468036 1.2 1 442448 25588 27 512154 1.2 1 478482 33672 28 492492 1.2 1 462349 30143 29 513596 1.2 1 476912 36684 30 549763 1.2 1 521613 28150 31 416541 1.2 1 392371 24170 32 537990 1.2 1 507240 30750 33 461062 1.2 1 434172 26890 34 514898 1.2 1 482060 32838 35 565682 1.2 1 527137 38545 36 520514 1.2 1 491038 29476 37 563159 1.2 1 535989 27170 38 400017 1.2 1 369694 30323 39 571304 1.2 1 535130 36174 40 474621 1.2 1 448623 25998 41 600561 1.2 1 562019 38542 42 458766 1.2 1 426402 32364 43 800955 1.2 1 763696 37259 44 235002 1.2 1 215582 19420 45 521706 1.2 1 491650 30056 46 537461 1.2 1 505916 31545 47 540258 1.2 1 510434 29824 48 449883 1.2 1 420809 29074 49 566867 1.2 1 529971 36896 50 457025 1.2 1 432856 24169 51 503689 1.2 1 474572 29117 52 554879 1.2 1 516852 38027 53 630277 1.2 1 598162 32115 54 395812 1.2 1 371351 24461 55 516387 1.2 1 488413 27974 56 554072 1.2 1 525098 28974 57 493826 1.2 1 465005 28821 58 455432 1.2 1 435241 20191 59 348004 1.2 1 326224 21780 60 524024 1.2 1 495485 28539 61 494677 1.2 1 470013 24664 62 445581 1.2 1 422101 23480 63 440868 1.2 1 415824 25044 64 419014 1.2 1 397741 21273 65 430484 1.2 1 407046 23438 66 478836 1.2 1 451552 27284 67 526917 1.2 1 490973 35944 68 974235 1.2 1 930569 43666 69 263384 1.2 1 246743 16641 70 78060 1.2 1 68230 9830 71 188944 1.2 1 177000 11944 72 350249 1.2 1 331713 18536 73 385004 1.2 1 364669 20335 74 373731 1.2 1 353304 20427 75 372636 1.2 1 352683 19953 76 364052 1.2 1 344608 19444 77 349658 1.2 1 330711 18947 78 336268 1.2 1 317764 18504 79 333907 1.2 1 315525 18382 80 320027 1.2 1 302554 17473 81 308343 1.2 1 291381 16962 82 303079 1.2 1 286638 16441 83 285198 1.2 1 269542 15656 84 281618 1.2 1 266189 15429 85 270078 1.2 1 255167 14911 86 256741 1.2 1 242477 14264 87 246300 1.2 1 232699 13601 88 239359 1.2 1 226087 13272 89 221157 1.2 1 208813 12344 90 214943 1.2 1 202774 12169 91 203469 1.2 1 192053 11416 92 193081 1.2 1 182042 11039 93 185749 1.2 1 175077 10672 94 173524 1.2 1 163677 9847 95 160182 1.2 1 150706 9476 96 148958 1.2 1 140034 8924 97 139705 1.2 1 131505 8200 98 129444 1.2 1 121874 7570 99 121244 1.2 1 114040 7204 100 113165 1.2 1 106483 6682 101 102845 1.2 1 96512 6333 102 94108 1.2 1 88374 5734 103 85449 1.2 1 80229 5220 104 76917 1.2 1 72056 4861 105 69454 1.2 1 64912 4542 106 62657 1.2 1 58630 4027 107 54683 1.2 1 51109 3574 108 49110 1.2 1 45908 3202 109 44137 1.2 1 41058 3079 110 38372 1.2 1 35617 2755 111 33619 1.2 1 31136 2483 112 30434 1.2 1 28239 2195 113 25366 1.2 1 23490 1876 114 23496 1.2 1 21717 1779 115 19033 1.2 1 17590 1443 116 16344 1.2 1 14972 1372 117 13454 1.2 1 12326 1128 118 11466 1.2 1 10507 959 119 8924 1.2 1 8136 788 120 8008 1.2 1 7309 699 121 6748 1.2 1 6146 602 122 5464 1.2 1 4939 525 123 4525 1.2 1 4074 451 124 3864 1.2 1 3437 427 125 3136 1.2 1 2820 316 126 2478 1.2 1 2171 307 127 2123 1.2 1 1865 258 128 1659 1.2 1 1463 196 129 1306 1.2 1 1161 145 130 1169 1.2 1 1027 142 131 997 1.2 1 875 122 132 756 1.2 1 652 104 133 674 1.2 1 579 95 134 665 1.2 1 580 85 135 442 1.2 1 374 68 136 281 1.2 1 246 35 137 223 1.2 1 178 45 138 175 1.2 1 145 30 139 132 1.2 1 108 24 140 105 1.2 1 88 17 141 84 1.2 1 61 23 142 69 1.2 1 59 10 143 49 1.2 1 38 11 144 68 1.2 1 56 12 145 42 1.2 1 31 11 146 49 1.2 1 40 9 147 75 1.2 1 67 8 148 68 1.2 1 58 10 149 58 1.2 1 50 8 150 375 1.2 1 309 66 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_L001_R1_001.fastq.gz ============================================= 82177525 sequences processed in total