SUMMARISING RUN PARAMETERS ========================== Input filename: A-N4371-1.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-N4371-1.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 979.09 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 26,949,042 Reads with adapters: 10,456,029 (38.8%) Reads written (passing filters): 26,949,042 (100.0%) Total basepairs processed: 1,741,149,641 bp Quality-trimmed: 102,944 bp (0.0%) Total written (filtered): 1,723,713,069 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10456029 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.5% C: 27.3% G: 23.0% T: 22.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8173969 6737260.5 0 8173969 2 1571657 1684315.1 0 1571657 3 427157 421078.8 0 427157 4 94990 105269.7 0 94990 5 24541 26317.4 0 24541 6 13801 6579.4 0 13801 7 4791 1644.8 0 4791 8 3615 411.2 0 3615 9 3551 102.8 0 2687 864 10 3577 25.7 1 2186 1391 11 4086 6.4 1 2437 1649 12 3546 1.6 1 2559 987 13 3148 1.6 1 2441 707 14 3606 1.6 1 2245 1361 15 3395 1.6 1 2072 1323 16 2650 1.6 1 1989 661 17 2739 1.6 1 2070 669 18 2516 1.6 1 2225 291 19 3085 1.6 1 2641 444 20 3271 1.6 1 2840 431 21 3448 1.6 1 3156 292 22 4509 1.6 1 3406 1103 23 4784 1.6 1 4377 407 24 4599 1.6 1 4209 390 25 3688 1.6 1 3366 322 26 3133 1.6 1 2791 342 27 3166 1.6 1 2716 450 28 3412 1.6 1 3027 385 29 3881 1.6 1 3493 388 30 4386 1.6 1 4028 358 31 4659 1.6 1 4326 333 32 4924 1.6 1 4606 318 33 8304 1.6 1 7786 518 34 3809 1.6 1 3478 331 35 6662 1.6 1 6303 359 36 3736 1.6 1 3378 358 37 3487 1.6 1 3221 266 38 5604 1.6 1 5171 433 39 1769 1.6 1 1524 245 40 2608 1.6 1 2270 338 41 1280 1.6 1 1013 267 42 898 1.6 1 703 195 43 1084 1.6 1 482 602 44 552 1.6 1 333 219 45 757 1.6 1 352 405 46 676 1.6 1 397 279 47 538 1.6 1 293 245 48 929 1.6 1 502 427 49 791 1.6 1 592 199 50 1844 1.6 1 68 1776 51 451 1.6 1 16 435 52 268 1.6 1 5 263 53 546 1.6 1 3 543 54 131 1.6 1 8 123 55 537 1.6 1 4 533 56 261 1.6 1 1 260 57 179 1.6 1 4 175 58 516 1.6 1 0 516 59 284 1.6 1 2 282 60 1223 1.6 1 6 1217 61 215 1.6 1 1 214 62 288 1.6 1 17 271 63 488 1.6 1 3 485 64 122 1.6 1 3 119 65 117 1.6 1 2 115 66 198 1.6 1 4 194 67 239 1.6 1 11 228 68 438 1.6 1 2 436 69 91 1.6 1 2 89 70 100 1.6 1 5 95 71 64 1.6 1 3 61 72 121 1.6 1 14 107 73 466 1.6 1 8 458 74 134 1.6 1 24 110 75 869 1.6 1 660 209 76 75 1.6 1 3 72 RUN STATISTICS FOR INPUT FILE: A-N4371-1.end2.fastq.gz ============================================= 26949042 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 26949042 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21880 (0.08%)