SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank3-15-16_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: 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_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 277.65 s (6 us/read; 10.70 M reads/minute). === Summary === Total reads processed: 49,500,297 Reads with adapters: 23,486,643 (47.4%) Reads written (passing filters): 49,500,297 (100.0%) Total basepairs processed: 7,425,044,550 bp Quality-trimmed: 121,639,790 bp (1.6%) Total written (filtered): 7,241,870,893 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23486643 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 18.9% G: 1.4% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21289627 12375074.2 0 21289627 2 336759 3093768.6 0 336759 3 160144 773442.1 0 160144 4 100727 193360.5 0 100727 5 81845 48340.1 0 81845 6 75315 12085.0 0 75315 7 81415 3021.3 0 81415 8 64466 755.3 0 64466 9 57809 188.8 0 57468 341 10 69497 47.2 1 65171 4326 11 53230 11.8 1 49300 3930 12 58629 3.0 1 54158 4471 13 53661 0.7 1 48925 4736 14 67055 0.7 1 61198 5857 15 40521 0.7 1 37362 3159 16 46829 0.7 1 43025 3804 17 52270 0.7 1 48559 3711 18 32250 0.7 1 29805 2445 19 45405 0.7 1 42052 3353 20 33630 0.7 1 31097 2533 21 29543 0.7 1 27378 2165 22 33323 0.7 1 30798 2525 23 32740 0.7 1 30110 2630 24 46971 0.7 1 43162 3809 25 24131 0.7 1 22207 1924 26 22258 0.7 1 20638 1620 27 21059 0.7 1 19441 1618 28 26017 0.7 1 24021 1996 29 19185 0.7 1 17595 1590 30 25656 0.7 1 23635 2021 31 15925 0.7 1 14731 1194 32 20115 0.7 1 18552 1563 33 17462 0.7 1 16079 1383 34 15023 0.7 1 13821 1202 35 17440 0.7 1 16052 1388 36 13511 0.7 1 12292 1219 37 12579 0.7 1 11466 1113 38 13097 0.7 1 11905 1192 39 11320 0.7 1 10370 950 40 11321 0.7 1 10265 1056 41 10896 0.7 1 9846 1050 42 11970 0.7 1 10798 1172 43 7986 0.7 1 7336 650 44 8955 0.7 1 8153 802 45 11644 0.7 1 10605 1039 46 6536 0.7 1 5879 657 47 5946 0.7 1 5432 514 48 8127 0.7 1 7364 763 49 6088 0.7 1 5540 548 50 5417 0.7 1 4853 564 51 13371 0.7 1 12335 1036 52 2618 0.7 1 2248 370 53 3351 0.7 1 2981 370 54 2903 0.7 1 2569 334 55 4952 0.7 1 4482 470 56 4450 0.7 1 3996 454 57 3728 0.7 1 3299 429 58 4353 0.7 1 3908 445 59 3783 0.7 1 3345 438 60 3781 0.7 1 3353 428 61 4856 0.7 1 4308 548 62 5810 0.7 1 5254 556 63 9697 0.7 1 8068 1629 64 44964 0.7 1 43397 1567 65 11794 0.7 1 11154 640 66 3884 0.7 1 3446 438 67 2695 0.7 1 2353 342 68 1851 0.7 1 1590 261 69 1394 0.7 1 1103 291 70 1196 0.7 1 939 257 71 1154 0.7 1 889 265 72 1263 0.7 1 1005 258 73 1290 0.7 1 1009 281 74 1329 0.7 1 1111 218 75 1184 0.7 1 946 238 76 1184 0.7 1 908 276 77 936 0.7 1 711 225 78 915 0.7 1 687 228 79 809 0.7 1 582 227 80 653 0.7 1 430 223 81 605 0.7 1 417 188 82 579 0.7 1 413 166 83 528 0.7 1 393 135 84 489 0.7 1 340 149 85 505 0.7 1 381 124 86 497 0.7 1 359 138 87 421 0.7 1 285 136 88 495 0.7 1 381 114 89 442 0.7 1 342 100 90 368 0.7 1 258 110 91 353 0.7 1 273 80 92 357 0.7 1 230 127 93 328 0.7 1 215 113 94 337 0.7 1 237 100 95 293 0.7 1 208 85 96 329 0.7 1 232 97 97 315 0.7 1 214 101 98 261 0.7 1 167 94 99 252 0.7 1 178 74 100 236 0.7 1 164 72 101 220 0.7 1 148 72 102 240 0.7 1 164 76 103 219 0.7 1 149 70 104 220 0.7 1 147 73 105 221 0.7 1 156 65 106 188 0.7 1 140 48 107 203 0.7 1 139 64 108 196 0.7 1 135 61 109 175 0.7 1 118 57 110 188 0.7 1 125 63 111 158 0.7 1 106 52 112 187 0.7 1 129 58 113 208 0.7 1 154 54 114 181 0.7 1 125 56 115 172 0.7 1 112 60 116 203 0.7 1 140 63 117 200 0.7 1 124 76 118 236 0.7 1 141 95 119 277 0.7 1 157 120 120 308 0.7 1 153 155 121 402 0.7 1 195 207 122 445 0.7 1 185 260 123 510 0.7 1 204 306 124 650 0.7 1 194 456 125 657 0.7 1 158 499 126 724 0.7 1 167 557 127 731 0.7 1 137 594 128 751 0.7 1 130 621 129 602 0.7 1 117 485 130 516 0.7 1 130 386 131 423 0.7 1 129 294 132 418 0.7 1 195 223 133 353 0.7 1 172 181 134 332 0.7 1 195 137 135 302 0.7 1 186 116 136 324 0.7 1 197 127 137 236 0.7 1 159 77 138 209 0.7 1 133 76 139 158 0.7 1 99 59 140 175 0.7 1 134 41 141 149 0.7 1 110 39 142 140 0.7 1 108 32 143 169 0.7 1 136 33 144 218 0.7 1 174 44 145 251 0.7 1 215 36 146 220 0.7 1 187 33 147 197 0.7 1 164 33 148 631 0.7 1 573 58 149 565 0.7 1 464 101 150 3522 0.7 1 3029 493 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank3-15-16_R2_001.fastq.gz ============================================= 49500297 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 49500297 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 212102 (0.43%)