SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_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: 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_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 363.11 s (5 us/read; 10.94 M reads/minute). === Summary === Total reads processed: 66,223,383 Reads with adapters: 31,829,733 (48.1%) Reads written (passing filters): 66,223,383 (100.0%) Total basepairs processed: 9,933,507,450 bp Quality-trimmed: 160,103,742 bp (1.6%) Total written (filtered): 9,679,575,690 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31829733 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 18.6% G: 1.2% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 28244968 16555845.8 0 28244968 2 429467 4138961.4 0 429467 3 232917 1034740.4 0 232917 4 159359 258685.1 0 159359 5 139016 64671.3 0 139016 6 128114 16167.8 0 128114 7 141832 4042.0 0 141832 8 111379 1010.5 0 111379 9 101142 252.6 0 100566 576 10 121587 63.2 1 114408 7179 11 93324 15.8 1 87164 6160 12 102994 3.9 1 95463 7531 13 95462 1.0 1 87430 8032 14 118718 1.0 1 108806 9912 15 72766 1.0 1 67382 5384 16 84508 1.0 1 77667 6841 17 93224 1.0 1 86970 6254 18 57987 1.0 1 53675 4312 19 82096 1.0 1 76393 5703 20 60967 1.0 1 56518 4449 21 53727 1.0 1 50007 3720 22 61243 1.0 1 56691 4552 23 59808 1.0 1 55177 4631 24 85681 1.0 1 78785 6896 25 44013 1.0 1 40993 3020 26 40191 1.0 1 37511 2680 27 38369 1.0 1 35692 2677 28 48061 1.0 1 44687 3374 29 35070 1.0 1 32522 2548 30 45731 1.0 1 42419 3312 31 29063 1.0 1 27063 2000 32 36556 1.0 1 33969 2587 33 31580 1.0 1 29277 2303 34 27409 1.0 1 25399 2010 35 31794 1.0 1 29547 2247 36 24458 1.0 1 22566 1892 37 23038 1.0 1 21263 1775 38 23570 1.0 1 21594 1976 39 20774 1.0 1 19196 1578 40 20585 1.0 1 18851 1734 41 19340 1.0 1 17798 1542 42 21015 1.0 1 19283 1732 43 14266 1.0 1 13158 1108 44 15741 1.0 1 14558 1183 45 18754 1.0 1 17275 1479 46 11524 1.0 1 10605 919 47 10952 1.0 1 10149 803 48 14208 1.0 1 13082 1126 49 10368 1.0 1 9538 830 50 9380 1.0 1 8510 870 51 21111 1.0 1 19603 1508 52 4383 1.0 1 3894 489 53 5542 1.0 1 5005 537 54 5227 1.0 1 4676 551 55 7897 1.0 1 7202 695 56 6850 1.0 1 6216 634 57 6105 1.0 1 5542 563 58 6667 1.0 1 6080 587 59 5919 1.0 1 5354 565 60 5837 1.0 1 5240 597 61 6339 1.0 1 5689 650 62 7568 1.0 1 6841 727 63 12167 1.0 1 10158 2009 64 55916 1.0 1 54024 1892 65 14586 1.0 1 13767 819 66 4745 1.0 1 4232 513 67 3370 1.0 1 2950 420 68 2235 1.0 1 1929 306 69 1803 1.0 1 1501 302 70 1413 1.0 1 1119 294 71 1358 1.0 1 1069 289 72 1498 1.0 1 1239 259 73 1566 1.0 1 1292 274 74 1495 1.0 1 1212 283 75 1437 1.0 1 1143 294 76 1362 1.0 1 1074 288 77 1169 1.0 1 932 237 78 960 1.0 1 711 249 79 925 1.0 1 704 221 80 795 1.0 1 586 209 81 693 1.0 1 481 212 82 649 1.0 1 459 190 83 659 1.0 1 456 203 84 596 1.0 1 418 178 85 555 1.0 1 399 156 86 555 1.0 1 396 159 87 543 1.0 1 382 161 88 570 1.0 1 425 145 89 494 1.0 1 365 129 90 435 1.0 1 323 112 91 443 1.0 1 318 125 92 432 1.0 1 310 122 93 391 1.0 1 276 115 94 406 1.0 1 279 127 95 365 1.0 1 257 108 96 356 1.0 1 242 114 97 350 1.0 1 231 119 98 305 1.0 1 225 80 99 286 1.0 1 205 81 100 280 1.0 1 217 63 101 309 1.0 1 217 92 102 301 1.0 1 199 102 103 288 1.0 1 198 90 104 261 1.0 1 185 76 105 261 1.0 1 184 77 106 240 1.0 1 161 79 107 223 1.0 1 145 78 108 206 1.0 1 132 74 109 197 1.0 1 124 73 110 237 1.0 1 146 91 111 173 1.0 1 129 44 112 239 1.0 1 172 67 113 247 1.0 1 172 75 114 252 1.0 1 186 66 115 247 1.0 1 173 74 116 260 1.0 1 174 86 117 252 1.0 1 156 96 118 262 1.0 1 143 119 119 278 1.0 1 146 132 120 380 1.0 1 167 213 121 477 1.0 1 203 274 122 550 1.0 1 199 351 123 651 1.0 1 224 427 124 757 1.0 1 211 546 125 827 1.0 1 176 651 126 887 1.0 1 156 731 127 877 1.0 1 156 721 128 896 1.0 1 131 765 129 860 1.0 1 174 686 130 629 1.0 1 136 493 131 508 1.0 1 154 354 132 447 1.0 1 182 265 133 523 1.0 1 258 265 134 468 1.0 1 247 221 135 457 1.0 1 265 192 136 407 1.0 1 241 166 137 323 1.0 1 208 115 138 296 1.0 1 204 92 139 255 1.0 1 188 67 140 236 1.0 1 169 67 141 190 1.0 1 141 49 142 174 1.0 1 129 45 143 157 1.0 1 125 32 144 204 1.0 1 159 45 145 265 1.0 1 228 37 146 232 1.0 1 189 43 147 273 1.0 1 227 46 148 860 1.0 1 790 70 149 662 1.0 1 546 116 150 4568 1.0 1 3977 591 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_R2_001.fastq.gz ============================================= 66223383 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 66223383 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 275977 (0.42%)