SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank3-15-16_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: 21510). 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/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/Tank3-15-16_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 263.37 s (5 us/read; 11.28 M reads/minute). === Summary === Total reads processed: 49,500,297 Reads with adapters: 20,259,602 (40.9%) Reads written (passing filters): 49,500,297 (100.0%) Total basepairs processed: 7,425,044,550 bp Quality-trimmed: 16,057,608 bp (0.2%) Total written (filtered): 7,345,703,020 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20259602 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.8% C: 9.6% G: 11.8% T: 45.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 14659319 12375074.2 0 14659319 2 2698496 3093768.6 0 2698496 3 873840 773442.1 0 873840 4 430145 193360.5 0 430145 5 79697 48340.1 0 79697 6 76201 12085.0 0 76201 7 74161 3021.3 0 74161 8 67129 755.3 0 67129 9 64797 188.8 0 64366 431 10 66690 47.2 1 63860 2830 11 59985 11.8 1 57906 2079 12 59057 3.0 1 56952 2105 13 54791 0.7 1 52897 1894 14 52990 0.7 1 51077 1913 15 50206 0.7 1 48431 1775 16 47298 0.7 1 45666 1632 17 46216 0.7 1 44521 1695 18 44776 0.7 1 43239 1537 19 39657 0.7 1 38308 1349 20 39059 0.7 1 37872 1187 21 37002 0.7 1 35615 1387 22 34867 0.7 1 33570 1297 23 32131 0.7 1 31151 980 24 31524 0.7 1 30463 1061 25 29611 0.7 1 28607 1004 26 26957 0.7 1 26060 897 27 25814 0.7 1 24961 853 28 24485 0.7 1 23628 857 29 22910 0.7 1 22173 737 30 22502 0.7 1 21775 727 31 19293 0.7 1 18683 610 32 18978 0.7 1 18395 583 33 17572 0.7 1 17034 538 34 16816 0.7 1 16294 522 35 15086 0.7 1 14665 421 36 14713 0.7 1 14239 474 37 13733 0.7 1 13297 436 38 14016 0.7 1 13565 451 39 10618 0.7 1 10313 305 40 11770 0.7 1 11357 413 41 10755 0.7 1 10439 316 42 8702 0.7 1 8419 283 43 12470 0.7 1 12135 335 44 5538 0.7 1 5332 206 45 6812 0.7 1 6661 151 46 7311 0.7 1 7118 193 47 6490 0.7 1 6317 173 48 6512 0.7 1 6316 196 49 5888 0.7 1 5671 217 50 5608 0.7 1 5427 181 51 5128 0.7 1 4983 145 52 5029 0.7 1 4847 182 53 5090 0.7 1 4933 157 54 3676 0.7 1 3552 124 55 4389 0.7 1 4255 134 56 3707 0.7 1 3598 109 57 3263 0.7 1 3156 107 58 3524 0.7 1 3422 102 59 2974 0.7 1 2886 88 60 2952 0.7 1 2855 97 61 3222 0.7 1 3118 104 62 2647 0.7 1 2556 91 63 2293 0.7 1 2190 103 64 2831 0.7 1 2708 123 65 2505 0.7 1 2394 111 66 2867 0.7 1 2583 284 67 5168 0.7 1 4928 240 68 3181 0.7 1 3061 120 69 4387 0.7 1 3851 536 70 36940 0.7 1 36450 490 71 7790 0.7 1 7609 181 72 2471 0.7 1 2369 102 73 1802 0.7 1 1737 65 74 1160 0.7 1 1098 62 75 1009 0.7 1 936 73 76 837 0.7 1 783 54 77 766 0.7 1 697 69 78 826 0.7 1 778 48 79 711 0.7 1 654 57 80 655 0.7 1 619 36 81 631 0.7 1 579 52 82 561 0.7 1 522 39 83 496 0.7 1 458 38 84 509 0.7 1 467 42 85 425 0.7 1 383 42 86 459 0.7 1 420 39 87 401 0.7 1 365 36 88 468 0.7 1 442 26 89 424 0.7 1 393 31 90 372 0.7 1 348 24 91 463 0.7 1 432 31 92 427 0.7 1 394 33 93 358 0.7 1 329 29 94 430 0.7 1 405 25 95 403 0.7 1 387 16 96 408 0.7 1 380 28 97 466 0.7 1 444 22 98 420 0.7 1 397 23 99 366 0.7 1 345 21 100 379 0.7 1 354 25 101 336 0.7 1 311 25 102 346 0.7 1 321 25 103 364 0.7 1 343 21 104 361 0.7 1 343 18 105 385 0.7 1 361 24 106 372 0.7 1 346 26 107 330 0.7 1 318 12 108 326 0.7 1 313 13 109 275 0.7 1 258 17 110 274 0.7 1 262 12 111 251 0.7 1 235 16 112 262 0.7 1 247 15 113 253 0.7 1 237 16 114 241 0.7 1 231 10 115 237 0.7 1 228 9 116 262 0.7 1 252 10 117 293 0.7 1 284 9 118 330 0.7 1 317 13 119 377 0.7 1 365 12 120 462 0.7 1 439 23 121 430 0.7 1 416 14 122 451 0.7 1 441 10 123 440 0.7 1 428 12 124 431 0.7 1 415 16 125 338 0.7 1 326 12 126 350 0.7 1 338 12 127 302 0.7 1 287 15 128 240 0.7 1 231 9 129 185 0.7 1 181 4 130 171 0.7 1 168 3 131 149 0.7 1 144 5 132 155 0.7 1 147 8 133 148 0.7 1 140 8 134 121 0.7 1 119 2 135 126 0.7 1 124 2 136 129 0.7 1 126 3 137 130 0.7 1 127 3 138 130 0.7 1 129 1 139 149 0.7 1 141 8 140 182 0.7 1 176 6 141 181 0.7 1 177 4 142 224 0.7 1 214 10 143 267 0.7 1 258 9 144 362 0.7 1 353 9 145 627 0.7 1 608 19 146 501 0.7 1 485 16 147 464 0.7 1 438 26 148 1603 0.7 1 1525 78 149 1135 0.7 1 1064 71 150 9484 0.7 1 8949 535 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank3-15-16_R1_001.fastq.gz ============================================= 49500297 sequences processed in total