SUMMARISING RUN PARAMETERS ========================== Input filename: A-13190-1.end2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA A-13190-1.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1225.25 s (37 us/read; 1.63 M reads/minute). === Summary === Total reads processed: 33,292,159 Reads with adapters: 13,083,141 (39.3%) Reads written (passing filters): 33,292,159 (100.0%) Total basepairs processed: 2,129,697,207 bp Quality-trimmed: 73,067 bp (0.0%) Total written (filtered): 2,108,445,746 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 13083141 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.6% C: 27.3% G: 23.2% T: 21.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10293876 8323039.8 0 10293876 2 1932822 2080759.9 0 1932822 3 524315 520190.0 0 524315 4 114114 130047.5 0 114114 5 29595 32511.9 0 29595 6 16436 8128.0 0 16436 7 5529 2032.0 0 5529 8 4112 508.0 0 4112 9 4087 127.0 0 3032 1055 10 4089 31.7 1 2479 1610 11 4971 7.9 1 2801 2170 12 4157 2.0 1 2964 1193 13 3836 2.0 1 2878 958 14 4432 2.0 1 2567 1865 15 3998 2.0 1 2328 1670 16 3102 2.0 1 2172 930 17 3023 2.0 1 2188 835 18 2829 2.0 1 2514 315 19 3641 2.0 1 2987 654 20 3755 2.0 1 3085 670 21 3907 2.0 1 3540 367 22 5642 2.0 1 4210 1432 23 6035 2.0 1 5554 481 24 6051 2.0 1 5508 543 25 4320 2.0 1 3971 349 26 3573 2.0 1 3130 443 27 3377 2.0 1 2877 500 28 3882 2.0 1 3347 535 29 4401 2.0 1 3883 518 30 4618 2.0 1 4264 354 31 4873 2.0 1 4476 397 32 5358 2.0 1 4904 454 33 9863 2.0 1 9243 620 34 4462 2.0 1 4076 386 35 7279 2.0 1 6851 428 36 3680 2.0 1 3278 402 37 3475 2.0 1 3182 293 38 5875 2.0 1 5377 498 39 1934 2.0 1 1650 284 40 2918 2.0 1 2590 328 41 1421 2.0 1 1133 288 42 1004 2.0 1 785 219 43 1145 2.0 1 474 671 44 691 2.0 1 418 273 45 838 2.0 1 304 534 46 689 2.0 1 311 378 47 529 2.0 1 268 261 48 1001 2.0 1 482 519 49 944 2.0 1 655 289 50 2269 2.0 1 77 2192 51 518 2.0 1 25 493 52 366 2.0 1 12 354 53 689 2.0 1 4 685 54 184 2.0 1 6 178 55 619 2.0 1 3 616 56 299 2.0 1 4 295 57 231 2.0 1 2 229 58 586 2.0 1 2 584 59 344 2.0 1 3 341 60 1415 2.0 1 1 1414 61 220 2.0 1 2 218 62 284 2.0 1 26 258 63 554 2.0 1 11 543 64 168 2.0 1 12 156 65 165 2.0 1 7 158 66 235 2.0 1 3 232 67 314 2.0 1 6 308 68 516 2.0 1 5 511 69 91 2.0 1 2 89 70 102 2.0 1 11 91 71 70 2.0 1 6 64 72 130 2.0 1 17 113 73 555 2.0 1 12 543 74 155 2.0 1 46 109 75 1446 2.0 1 1183 263 76 112 2.0 1 12 100 RUN STATISTICS FOR INPUT FILE: A-13190-1.end2.fastq.gz ============================================= 33292159 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 33292159 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 25854 (0.08%)