SUMMARISING RUN PARAMETERS ========================== Input filename: A-13190-2.end1.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-13190-2.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 964.46 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 26,922,264 Reads with adapters: 10,524,822 (39.1%) Reads written (passing filters): 26,922,264 (100.0%) Total basepairs processed: 1,739,853,165 bp Quality-trimmed: 13,793 bp (0.0%) Total written (filtered): 1,721,996,494 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10524822 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.3% C: 27.6% G: 23.1% T: 22.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8217237 6730566.0 0 8217237 2 1584830 1682641.5 0 1584830 3 425548 420660.4 0 425548 4 94161 105165.1 0 94161 5 24206 26291.3 0 24206 6 13060 6572.8 0 13060 7 4931 1643.2 0 4931 8 3829 410.8 0 3829 9 3727 102.7 0 2905 822 10 3722 25.7 1 2580 1142 11 4415 6.4 1 2909 1506 12 3847 1.6 1 2932 915 13 3670 1.6 1 3015 655 14 4183 1.6 1 2772 1411 15 3730 1.6 1 2411 1319 16 2904 1.6 1 2259 645 17 2920 1.6 1 2337 583 18 2902 1.6 1 2694 208 19 3349 1.6 1 2935 414 20 3698 1.6 1 3226 472 21 4068 1.6 1 3761 307 22 5516 1.6 1 4340 1176 23 5666 1.6 1 5326 340 24 5520 1.6 1 5180 340 25 4345 1.6 1 4134 211 26 3489 1.6 1 3233 256 27 3374 1.6 1 2945 429 28 3581 1.6 1 3262 319 29 4331 1.6 1 4033 298 30 4714 1.6 1 4508 206 31 4636 1.6 1 4425 211 32 5050 1.6 1 4817 233 33 7035 1.6 1 6723 312 34 7420 1.6 1 7135 285 35 6555 1.6 1 6333 222 36 4792 1.6 1 4512 280 37 3700 1.6 1 3539 161 38 4114 1.6 1 3826 288 39 3740 1.6 1 3538 202 40 2782 1.6 1 2526 256 41 1635 1.6 1 1445 190 42 1029 1.6 1 854 175 43 1374 1.6 1 794 580 44 487 1.6 1 253 234 45 710 1.6 1 298 412 46 521 1.6 1 258 263 47 443 1.6 1 248 195 48 838 1.6 1 442 396 49 1084 1.6 1 867 217 50 2076 1.6 1 100 1976 51 419 1.6 1 20 399 52 247 1.6 1 6 241 53 583 1.6 1 3 580 54 161 1.6 1 5 156 55 544 1.6 1 2 542 56 244 1.6 1 4 240 57 180 1.6 1 0 180 58 502 1.6 1 4 498 59 267 1.6 1 1 266 60 1336 1.6 1 0 1336 61 208 1.6 1 0 208 62 266 1.6 1 37 229 63 549 1.6 1 1 548 64 121 1.6 1 7 114 65 155 1.6 1 6 149 66 182 1.6 1 5 177 67 256 1.6 1 6 250 68 495 1.6 1 5 490 69 79 1.6 1 1 78 70 94 1.6 1 2 92 71 54 1.6 1 6 48 72 105 1.6 1 7 98 73 512 1.6 1 5 507 74 144 1.6 1 42 102 75 1539 1.6 1 1335 204 76 86 1.6 1 3 83 RUN STATISTICS FOR INPUT FILE: A-13190-2.end1.fastq.gz ============================================= 26922264 sequences processed in total