SUMMARISING RUN PARAMETERS ========================== Input filename: A-13189-2.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-13189-2.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 932.44 s (37 us/read; 1.63 M reads/minute). === Summary === Total reads processed: 25,336,192 Reads with adapters: 9,912,139 (39.1%) Reads written (passing filters): 25,336,192 (100.0%) Total basepairs processed: 1,636,016,417 bp Quality-trimmed: 85,237 bp (0.0%) Total written (filtered): 1,619,168,208 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 9912139 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.4% C: 27.7% G: 23.1% T: 21.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7770009 6334048.0 0 7770009 2 1473403 1583512.0 0 1473403 3 391630 395878.0 0 391630 4 86215 98969.5 0 86215 5 22320 24742.4 0 22320 6 11849 6185.6 0 11849 7 4563 1546.4 0 4563 8 3567 386.6 0 3567 9 3623 96.6 0 2844 779 10 3568 24.2 1 2466 1102 11 4157 6.0 1 2648 1509 12 3700 1.5 1 2754 946 13 3540 1.5 1 2815 725 14 3896 1.5 1 2519 1377 15 3711 1.5 1 2349 1362 16 2810 1.5 1 2113 697 17 2723 1.5 1 2096 627 18 2660 1.5 1 2404 256 19 3345 1.5 1 2868 477 20 3296 1.5 1 2838 458 21 3724 1.5 1 3382 342 22 5196 1.5 1 4071 1125 23 5256 1.5 1 4868 388 24 5449 1.5 1 5020 429 25 4005 1.5 1 3739 266 26 3263 1.5 1 2912 351 27 3291 1.5 1 2854 437 28 3592 1.5 1 3175 417 29 4029 1.5 1 3624 405 30 4375 1.5 1 4094 281 31 4611 1.5 1 4256 355 32 4949 1.5 1 4600 349 33 9309 1.5 1 8765 544 34 3989 1.5 1 3647 342 35 7234 1.5 1 6845 389 36 3649 1.5 1 3305 344 37 3276 1.5 1 3026 250 38 5532 1.5 1 5142 390 39 1706 1.5 1 1470 236 40 2655 1.5 1 2403 252 41 1291 1.5 1 1068 223 42 890 1.5 1 710 180 43 1113 1.5 1 499 614 44 625 1.5 1 418 207 45 692 1.5 1 327 365 46 595 1.5 1 338 257 47 429 1.5 1 249 180 48 860 1.5 1 483 377 49 895 1.5 1 670 225 50 1952 1.5 1 75 1877 51 398 1.5 1 15 383 52 287 1.5 1 10 277 53 621 1.5 1 5 616 54 118 1.5 1 10 108 55 544 1.5 1 3 541 56 278 1.5 1 7 271 57 173 1.5 1 4 169 58 517 1.5 1 6 511 59 321 1.5 1 2 319 60 1373 1.5 1 3 1370 61 211 1.5 1 0 211 62 267 1.5 1 26 241 63 532 1.5 1 8 524 64 132 1.5 1 8 124 65 132 1.5 1 2 130 66 170 1.5 1 4 166 67 257 1.5 1 0 257 68 448 1.5 1 3 445 69 79 1.5 1 7 72 70 84 1.5 1 6 78 71 46 1.5 1 6 40 72 81 1.5 1 8 73 73 482 1.5 1 11 471 74 153 1.5 1 39 114 75 1344 1.5 1 1104 240 76 74 1.5 1 1 73 RUN STATISTICS FOR INPUT FILE: A-13189-2.end2.fastq.gz ============================================= 25336192 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 25336192 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21370 (0.08%)