SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P02-CTTGTA-READ1-Sequences.txt.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 Read 1 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 4 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 4 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /mnt/data/coral_RNAseq_2017/montipora/20180415_trimmed/fastqc --threads 24 Output file will be GZIP compressed This is cutadapt 1.16 with Python 3.6.4 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P02-CTTGTA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 652.60 s (20 us/read; 3.04 M reads/minute). === Summary === Total reads processed: 33,011,434 Reads with adapters: 11,622,689 (35.2%) Reads written (passing filters): 33,011,434 (100.0%) Total basepairs processed: 3,301,143,400 bp Quality-trimmed: 5,094,712 bp (0.2%) Total written (filtered): 3,267,700,214 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11622689 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 29.1% G: 17.0% T: 18.5% none/other: 0.8% Overview of removed sequences length count expect max.err error counts 1 8636441 8252858.5 0 8636441 2 1896262 2063214.6 0 1896262 3 540781 515803.7 0 540781 4 144408 128950.9 0 144408 5 48833 32237.7 0 48833 6 21534 8059.4 0 21534 7 17265 2014.9 0 17265 8 15126 503.7 0 15126 9 14576 125.9 0 14081 495 10 17688 31.5 1 12928 4760 11 12051 7.9 1 11337 714 12 11099 2.0 1 10527 572 13 10328 0.5 1 9781 547 14 9686 0.5 1 9203 483 15 9269 0.5 1 8823 446 16 8526 0.5 1 8051 475 17 7904 0.5 1 7453 451 18 7587 0.5 1 7170 417 19 6798 0.5 1 6421 377 20 5933 0.5 1 5628 305 21 5492 0.5 1 5173 319 22 4768 0.5 1 4500 268 23 4284 0.5 1 4086 198 24 4027 0.5 1 3813 214 25 3574 0.5 1 3355 219 26 3440 0.5 1 3272 168 27 3185 0.5 1 2996 189 28 3070 0.5 1 2888 182 29 2881 0.5 1 2717 164 30 2648 0.5 1 2504 144 31 2483 0.5 1 2329 154 32 2311 0.5 1 2188 123 33 2071 0.5 1 1939 132 34 1958 0.5 1 1817 141 35 1763 0.5 1 1641 122 36 1704 0.5 1 1590 114 37 1536 0.5 1 1412 124 38 1370 0.5 1 1279 91 39 1318 0.5 1 1204 114 40 1149 0.5 1 1048 101 41 1481 0.5 1 1351 130 42 574 0.5 1 527 47 43 709 0.5 1 655 54 44 717 0.5 1 644 73 45 775 0.5 1 711 64 46 678 0.5 1 612 66 47 702 0.5 1 637 65 48 683 0.5 1 613 70 49 635 0.5 1 579 56 50 654 0.5 1 596 58 51 562 0.5 1 514 48 52 528 0.5 1 452 76 53 547 0.5 1 476 71 54 427 0.5 1 361 66 55 428 0.5 1 387 41 56 380 0.5 1 316 64 57 351 0.5 1 312 39 58 367 0.5 1 316 51 59 315 0.5 1 264 51 60 293 0.5 1 238 55 61 294 0.5 1 248 46 62 288 0.5 1 247 41 63 280 0.5 1 239 41 64 323 0.5 1 273 50 65 357 0.5 1 298 59 66 320 0.5 1 260 60 67 349 0.5 1 281 68 68 376 0.5 1 311 65 69 509 0.5 1 416 93 70 459 0.5 1 333 126 71 590 0.5 1 383 207 72 964 0.5 1 406 558 73 9286 0.5 1 598 8688 74 16581 0.5 1 2178 14403 75 14773 0.5 1 2887 11886 76 10628 0.5 1 2342 8286 77 7552 0.5 1 1856 5696 78 4894 0.5 1 1234 3660 79 3478 0.5 1 865 2613 80 2565 0.5 1 660 1905 81 1763 0.5 1 525 1238 82 1224 0.5 1 379 845 83 1015 0.5 1 376 639 84 855 0.5 1 353 502 85 707 0.5 1 344 363 86 674 0.5 1 351 323 87 454 0.5 1 217 237 88 453 0.5 1 265 188 89 425 0.5 1 243 182 90 374 0.5 1 196 178 91 434 0.5 1 241 193 92 315 0.5 1 153 162 93 304 0.5 1 126 178 94 400 0.5 1 139 261 95 501 0.5 1 215 286 96 611 0.5 1 243 368 97 910 0.5 1 315 595 98 986 0.5 1 188 798 99 2673 0.5 1 91 2582 100 23812 0.5 1 130 23682 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P02-CTTGTA-READ1-Sequences.txt.gz ============================================= 33011434 sequences processed in total