SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_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: 28091). 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/20200930/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/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 355.15 s (5 us/read; 11.19 M reads/minute). === Summary === Total reads processed: 66,223,383 Reads with adapters: 27,658,950 (41.8%) Reads written (passing filters): 66,223,383 (100.0%) Total basepairs processed: 9,933,507,450 bp Quality-trimmed: 21,039,090 bp (0.2%) Total written (filtered): 9,814,871,032 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 27658950 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.0% C: 11.6% G: 11.3% T: 45.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19501425 16555845.8 0 19501425 2 3563434 4138961.4 0 3563434 3 1191860 1034740.4 0 1191860 4 601115 258685.1 0 601115 5 137950 64671.3 0 137950 6 129643 16167.8 0 129643 7 125732 4042.0 0 125732 8 116894 1010.5 0 116894 9 116013 252.6 0 115476 537 10 115995 63.2 1 111576 4419 11 107740 15.8 1 104168 3572 12 104712 3.9 1 101085 3627 13 97711 1.0 1 94472 3239 14 94151 1.0 1 90888 3263 15 89500 1.0 1 86547 2953 16 87184 1.0 1 84023 3161 17 83306 1.0 1 80034 3272 18 85473 1.0 1 82458 3015 19 68634 1.0 1 66457 2177 20 71619 1.0 1 69330 2289 21 65217 1.0 1 63116 2101 22 63324 1.0 1 61228 2096 23 59457 1.0 1 57591 1866 24 57987 1.0 1 55849 2138 25 54180 1.0 1 52393 1787 26 50343 1.0 1 48646 1697 27 47373 1.0 1 45902 1471 28 45334 1.0 1 43874 1460 29 42891 1.0 1 41412 1479 30 39436 1.0 1 38269 1167 31 37731 1.0 1 36533 1198 32 35069 1.0 1 34030 1039 33 31900 1.0 1 31042 858 34 31517 1.0 1 30493 1024 35 28093 1.0 1 27352 741 36 27147 1.0 1 26302 845 37 25905 1.0 1 25075 830 38 23679 1.0 1 22990 689 39 22739 1.0 1 22036 703 40 20221 1.0 1 19621 600 41 19934 1.0 1 19327 607 42 16630 1.0 1 16157 473 43 23070 1.0 1 22493 577 44 9939 1.0 1 9611 328 45 12255 1.0 1 11957 298 46 13058 1.0 1 12706 352 47 11794 1.0 1 11469 325 48 11658 1.0 1 11350 308 49 10341 1.0 1 10036 305 50 9785 1.0 1 9512 273 51 9015 1.0 1 8745 270 52 8801 1.0 1 8540 261 53 9137 1.0 1 8870 267 54 6482 1.0 1 6308 174 55 7287 1.0 1 7063 224 56 6275 1.0 1 6093 182 57 5382 1.0 1 5226 156 58 6088 1.0 1 5934 154 59 4879 1.0 1 4744 135 60 4798 1.0 1 4661 137 61 5243 1.0 1 5070 173 62 4199 1.0 1 4065 134 63 3455 1.0 1 3333 122 64 4051 1.0 1 3874 177 65 3720 1.0 1 3570 150 66 4129 1.0 1 3749 380 67 6286 1.0 1 6054 232 68 4503 1.0 1 4330 173 69 5657 1.0 1 5036 621 70 43977 1.0 1 43428 549 71 9527 1.0 1 9308 219 72 3040 1.0 1 2915 125 73 2231 1.0 1 2143 88 74 1556 1.0 1 1474 82 75 1348 1.0 1 1268 80 76 1113 1.0 1 1049 64 77 997 1.0 1 937 60 78 915 1.0 1 850 65 79 968 1.0 1 893 75 80 952 1.0 1 883 69 81 827 1.0 1 773 54 82 744 1.0 1 692 52 83 679 1.0 1 633 46 84 619 1.0 1 568 51 85 626 1.0 1 581 45 86 597 1.0 1 546 51 87 535 1.0 1 495 40 88 527 1.0 1 491 36 89 502 1.0 1 463 39 90 506 1.0 1 481 25 91 602 1.0 1 563 39 92 509 1.0 1 480 29 93 487 1.0 1 459 28 94 491 1.0 1 457 34 95 491 1.0 1 462 29 96 476 1.0 1 443 33 97 580 1.0 1 544 36 98 486 1.0 1 459 27 99 451 1.0 1 425 26 100 439 1.0 1 409 30 101 441 1.0 1 409 32 102 437 1.0 1 412 25 103 426 1.0 1 396 30 104 445 1.0 1 424 21 105 462 1.0 1 439 23 106 498 1.0 1 481 17 107 468 1.0 1 446 22 108 390 1.0 1 371 19 109 358 1.0 1 341 17 110 352 1.0 1 333 19 111 352 1.0 1 324 28 112 409 1.0 1 394 15 113 382 1.0 1 364 18 114 378 1.0 1 352 26 115 327 1.0 1 314 13 116 343 1.0 1 329 14 117 355 1.0 1 344 11 118 401 1.0 1 390 11 119 445 1.0 1 426 19 120 505 1.0 1 491 14 121 543 1.0 1 525 18 122 485 1.0 1 470 15 123 537 1.0 1 529 8 124 498 1.0 1 487 11 125 453 1.0 1 448 5 126 418 1.0 1 411 7 127 379 1.0 1 378 1 128 293 1.0 1 287 6 129 221 1.0 1 216 5 130 193 1.0 1 189 4 131 205 1.0 1 200 5 132 210 1.0 1 204 6 133 161 1.0 1 159 2 134 139 1.0 1 132 7 135 150 1.0 1 143 7 136 141 1.0 1 139 2 137 176 1.0 1 169 7 138 144 1.0 1 141 3 139 195 1.0 1 189 6 140 188 1.0 1 186 2 141 261 1.0 1 256 5 142 240 1.0 1 235 5 143 330 1.0 1 319 11 144 423 1.0 1 410 13 145 623 1.0 1 608 15 146 578 1.0 1 556 22 147 606 1.0 1 578 28 148 2146 1.0 1 2057 89 149 1639 1.0 1 1570 69 150 12918 1.0 1 12280 638 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_R1_001.fastq.gz ============================================= 66223383 sequences processed in total