SUMMARISING RUN PARAMETERS ========================== Input filename: A-15171-2.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-15171-2.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 913.24 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 25,447,185 Reads with adapters: 10,033,482 (39.4%) Reads written (passing filters): 25,447,185 (100.0%) Total basepairs processed: 1,624,817,394 bp Quality-trimmed: 104,398 bp (0.0%) Total written (filtered): 1,607,075,227 bp (98.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10033482 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.8% C: 27.5% G: 23.1% T: 21.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7885174 6361796.2 0 7885174 2 1460509 1590449.1 0 1460509 3 380998 397612.3 0 380998 4 83591 99403.1 0 83591 5 21877 24850.8 0 21877 6 12085 6212.7 0 12085 7 4985 1553.2 0 4985 8 4216 388.3 0 4216 9 4154 97.1 0 3424 730 10 4196 24.3 1 2964 1232 11 4910 6.1 1 3154 1756 12 4521 1.5 1 3410 1111 13 4245 1.5 1 3524 721 14 4670 1.5 1 3107 1563 15 4343 1.5 1 2870 1473 16 3547 1.5 1 2730 817 17 3419 1.5 1 2765 654 18 3267 1.5 1 2992 275 19 4122 1.5 1 3567 555 20 4225 1.5 1 3693 532 21 4714 1.5 1 4418 296 22 6276 1.5 1 4958 1318 23 6585 1.5 1 6169 416 24 6641 1.5 1 6151 490 25 5106 1.5 1 4815 291 26 4086 1.5 1 3768 318 27 4159 1.5 1 3681 478 28 4647 1.5 1 4201 446 29 5273 1.5 1 4841 432 30 5678 1.5 1 5356 322 31 5973 1.5 1 5568 405 32 6324 1.5 1 5946 378 33 11477 1.5 1 10920 557 34 5026 1.5 1 4687 339 35 9067 1.5 1 8664 403 36 4625 1.5 1 4301 324 37 4257 1.5 1 3986 271 38 6915 1.5 1 6446 469 39 2096 1.5 1 1820 276 40 3018 1.5 1 2740 278 41 1291 1.5 1 1094 197 42 905 1.5 1 694 211 43 951 1.5 1 469 482 44 574 1.5 1 373 201 45 801 1.5 1 392 409 46 697 1.5 1 412 285 47 556 1.5 1 311 245 48 950 1.5 1 581 369 49 1017 1.5 1 790 227 50 1975 1.5 1 105 1870 51 376 1.5 1 16 360 52 294 1.5 1 7 287 53 532 1.5 1 9 523 54 139 1.5 1 5 134 55 503 1.5 1 1 502 56 224 1.5 1 3 221 57 167 1.5 1 6 161 58 453 1.5 1 1 452 59 334 1.5 1 9 325 60 1172 1.5 1 2 1170 61 172 1.5 1 4 168 62 233 1.5 1 26 207 63 453 1.5 1 5 448 64 104 1.5 1 10 94 65 150 1.5 1 5 145 66 139 1.5 1 2 137 67 252 1.5 1 4 248 68 424 1.5 1 5 419 69 78 1.5 1 6 72 70 94 1.5 1 13 81 71 57 1.5 1 7 50 72 101 1.5 1 16 85 73 394 1.5 1 13 381 74 148 1.5 1 41 107 75 1691 1.5 1 1450 241 76 84 1.5 1 5 79 RUN STATISTICS FOR INPUT FILE: A-15171-2.end2.fastq.gz ============================================= 25447185 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 25447185 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21830 (0.09%)