SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_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: 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_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 354.89 s (4 us/read; 13.89 M reads/minute). === Summary === Total reads processed: 82,177,525 Reads with adapters: 58,336,382 (71.0%) Reads written (passing filters): 82,177,525 (100.0%) Total basepairs processed: 12,326,628,750 bp Quality-trimmed: 41,419,626 bp (0.3%) Total written (filtered): 10,364,431,817 bp (84.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58336382 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: 34.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15350057 20544381.2 0 15350057 2 1685474 5136095.3 0 1685474 3 903882 1284023.8 0 903882 4 571222 321006.0 0 571222 5 501936 80251.5 0 501936 6 415827 20062.9 0 415827 7 347542 5015.7 0 347542 8 483968 1253.9 0 483968 9 396796 313.5 0 395692 1104 10 420274 78.4 1 402160 18114 11 438864 19.6 1 414608 24256 12 449536 4.9 1 424165 25371 13 510213 1.2 1 482515 27698 14 455618 1.2 1 427602 28016 15 389210 1.2 1 366432 22778 16 555171 1.2 1 523342 31829 17 419400 1.2 1 394087 25313 18 418646 1.2 1 395171 23475 19 509488 1.2 1 480141 29347 20 480908 1.2 1 453798 27110 21 427296 1.2 1 402705 24591 22 474401 1.2 1 448452 25949 23 490252 1.2 1 461826 28426 24 484904 1.2 1 457572 27332 25 539104 1.2 1 510128 28976 26 453073 1.2 1 425411 27662 27 501857 1.2 1 468630 33227 28 457877 1.2 1 436189 21688 29 491156 1.2 1 462299 28857 30 462417 1.2 1 439850 22567 31 522905 1.2 1 492898 30007 32 460424 1.2 1 437863 22561 33 512386 1.2 1 483241 29145 34 657426 1.2 1 620019 37407 35 363385 1.2 1 345024 18361 36 487371 1.2 1 459211 28160 37 533683 1.2 1 504069 29614 38 481104 1.2 1 458652 22452 39 485376 1.2 1 462217 23159 40 532302 1.2 1 503234 29068 41 511389 1.2 1 485806 25583 42 521546 1.2 1 495601 25945 43 480650 1.2 1 455868 24782 44 546125 1.2 1 517755 28370 45 570120 1.2 1 542069 28051 46 418884 1.2 1 397786 21098 47 505326 1.2 1 481272 24054 48 488484 1.2 1 466397 22087 49 514214 1.2 1 489094 25120 50 501739 1.2 1 476010 25729 51 610289 1.2 1 580951 29338 52 441047 1.2 1 421068 19979 53 520314 1.2 1 497213 23101 54 398195 1.2 1 379916 18279 55 496805 1.2 1 475323 21482 56 496057 1.2 1 473000 23057 57 480165 1.2 1 458650 21515 58 465002 1.2 1 445044 19958 59 473368 1.2 1 452197 21171 60 477456 1.2 1 455816 21640 61 491054 1.2 1 468379 22675 62 525084 1.2 1 500148 24936 63 688105 1.2 1 659460 28645 64 513363 1.2 1 493656 19707 65 351437 1.2 1 336316 15121 66 388237 1.2 1 371824 16413 67 391608 1.2 1 373999 17609 68 389520 1.2 1 372639 16881 69 387449 1.2 1 370434 17015 70 386662 1.2 1 369736 16926 71 401493 1.2 1 384632 16861 72 387884 1.2 1 370945 16939 73 410793 1.2 1 393742 17051 74 371310 1.2 1 356033 15277 75 357117 1.2 1 342286 14831 76 343694 1.2 1 329251 14443 77 331451 1.2 1 317224 14227 78 322073 1.2 1 308399 13674 79 311753 1.2 1 298772 12981 80 303996 1.2 1 291594 12402 81 292352 1.2 1 280150 12202 82 283173 1.2 1 271407 11766 83 268006 1.2 1 256925 11081 84 264798 1.2 1 253456 11342 85 258296 1.2 1 247093 11203 86 251541 1.2 1 240826 10715 87 251948 1.2 1 241533 10415 88 239999 1.2 1 230066 9933 89 210279 1.2 1 201522 8757 90 198432 1.2 1 189963 8469 91 186654 1.2 1 178634 8020 92 175644 1.2 1 168171 7473 93 173446 1.2 1 166287 7159 94 161637 1.2 1 154843 6794 95 151052 1.2 1 144859 6193 96 140237 1.2 1 134508 5729 97 130886 1.2 1 125542 5344 98 122501 1.2 1 117472 5029 99 115054 1.2 1 110586 4468 100 107801 1.2 1 103547 4254 101 95638 1.2 1 91917 3721 102 87834 1.2 1 84365 3469 103 80762 1.2 1 77514 3248 104 75976 1.2 1 73089 2887 105 67619 1.2 1 64884 2735 106 60836 1.2 1 58481 2355 107 52108 1.2 1 50074 2034 108 45224 1.2 1 43372 1852 109 41239 1.2 1 39535 1704 110 35967 1.2 1 34472 1495 111 33060 1.2 1 31766 1294 112 29404 1.2 1 28175 1229 113 24708 1.2 1 23673 1035 114 22438 1.2 1 21537 901 115 17752 1.2 1 17001 751 116 15010 1.2 1 14377 633 117 12079 1.2 1 11520 559 118 10437 1.2 1 9967 470 119 8208 1.2 1 7826 382 120 7212 1.2 1 6891 321 121 6273 1.2 1 5988 285 122 5055 1.2 1 4818 237 123 4309 1.2 1 4110 199 124 3571 1.2 1 3389 182 125 2948 1.2 1 2833 115 126 2296 1.2 1 2182 114 127 1959 1.2 1 1851 108 128 1542 1.2 1 1473 69 129 1221 1.2 1 1160 61 130 1047 1.2 1 984 63 131 945 1.2 1 892 53 132 678 1.2 1 641 37 133 631 1.2 1 593 38 134 648 1.2 1 616 32 135 387 1.2 1 364 23 136 258 1.2 1 239 19 137 195 1.2 1 184 11 138 163 1.2 1 151 12 139 116 1.2 1 108 8 140 92 1.2 1 83 9 141 73 1.2 1 63 10 142 63 1.2 1 54 9 143 46 1.2 1 37 9 144 54 1.2 1 48 6 145 44 1.2 1 35 9 146 46 1.2 1 42 4 147 78 1.2 1 75 3 148 63 1.2 1 57 6 149 48 1.2 1 46 2 150 297 1.2 1 280 17 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Caligus/FASTQS/RAW/Sealice_F2_S22_L001_R2_001.fastq.gz ============================================= 82177525 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82177525 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 351178 (0.43%)