SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P01-AGTCAA-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-P01-AGTCAA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 499.01 s (20 us/read; 3.03 M reads/minute). === Summary === Total reads processed: 25,174,276 Reads with adapters: 9,421,305 (37.4%) Reads written (passing filters): 25,174,276 (100.0%) Total basepairs processed: 2,517,427,600 bp Quality-trimmed: 2,170,846 bp (0.1%) Total written (filtered): 2,493,300,443 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9421305 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 26.9% G: 18.2% T: 18.4% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 6791104 6293569.0 0 6791104 2 1586895 1573392.2 0 1586895 3 500638 393348.1 0 500638 4 141680 98337.0 0 141680 5 48168 24584.3 0 48168 6 25528 6146.1 0 25528 7 20842 1536.5 0 20842 8 18780 384.1 0 18780 9 18156 96.0 0 17560 596 10 19214 24.0 1 15677 3537 11 14672 6.0 1 13908 764 12 13493 1.5 1 12861 632 13 12774 0.4 1 12162 612 14 11859 0.4 1 11282 577 15 11493 0.4 1 10936 557 16 10788 0.4 1 10226 562 17 10079 0.4 1 9588 491 18 9811 0.4 1 9324 487 19 8390 0.4 1 7954 436 20 7699 0.4 1 7316 383 21 6759 0.4 1 6411 348 22 5949 0.4 1 5617 332 23 5242 0.4 1 4975 267 24 4832 0.4 1 4562 270 25 4429 0.4 1 4207 222 26 4190 0.4 1 3997 193 27 4011 0.4 1 3826 185 28 3749 0.4 1 3550 199 29 3595 0.4 1 3405 190 30 3337 0.4 1 3131 206 31 2869 0.4 1 2724 145 32 2880 0.4 1 2736 144 33 2489 0.4 1 2364 125 34 2423 0.4 1 2279 144 35 2168 0.4 1 2055 113 36 2221 0.4 1 2088 133 37 1838 0.4 1 1729 109 38 1837 0.4 1 1729 108 39 1626 0.4 1 1508 118 40 1409 0.4 1 1292 117 41 1330 0.4 1 1236 94 42 1178 0.4 1 1082 96 43 1593 0.4 1 1462 131 44 535 0.4 1 483 52 45 764 0.4 1 723 41 46 800 0.4 1 751 49 47 827 0.4 1 769 58 48 942 0.4 1 859 83 49 821 0.4 1 743 78 50 810 0.4 1 738 72 51 779 0.4 1 728 51 52 725 0.4 1 665 60 53 639 0.4 1 588 51 54 653 0.4 1 580 73 55 657 0.4 1 588 69 56 425 0.4 1 369 56 57 501 0.4 1 452 49 58 457 0.4 1 414 43 59 491 0.4 1 444 47 60 502 0.4 1 443 59 61 434 0.4 1 391 43 62 481 0.4 1 429 52 63 418 0.4 1 383 35 64 449 0.4 1 393 56 65 473 0.4 1 420 53 66 534 0.4 1 461 73 67 475 0.4 1 406 69 68 523 0.4 1 485 38 69 667 0.4 1 593 74 70 571 0.4 1 522 49 71 610 0.4 1 563 47 72 606 0.4 1 534 72 73 688 0.4 1 585 103 74 803 0.4 1 621 182 75 3256 0.4 1 799 2457 76 6034 0.4 1 2255 3779 77 6595 0.4 1 2787 3808 78 5470 0.4 1 2383 3087 79 4195 0.4 1 1943 2252 80 2952 0.4 1 1459 1493 81 2006 0.4 1 991 1015 82 1482 0.4 1 778 704 83 1065 0.4 1 609 456 84 783 0.4 1 468 315 85 656 0.4 1 407 249 86 654 0.4 1 457 197 87 485 0.4 1 333 152 88 433 0.4 1 311 122 89 376 0.4 1 258 118 90 311 0.4 1 212 99 91 355 0.4 1 262 93 92 249 0.4 1 178 71 93 252 0.4 1 171 81 94 221 0.4 1 129 92 95 300 0.4 1 193 107 96 326 0.4 1 171 155 97 560 0.4 1 342 218 98 425 0.4 1 144 281 99 979 0.4 1 79 900 100 7808 0.4 1 94 7714 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P01-AGTCAA-READ1-Sequences.txt.gz ============================================= 25174276 sequences processed in total