SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P05-GAGTGG-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/porites/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/porites/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 536.88 s (20 us/read; 2.99 M reads/minute). === Summary === Total reads processed: 26,724,234 Reads with adapters: 10,486,555 (39.2%) Reads written (passing filters): 26,724,234 (100.0%) Total basepairs processed: 2,672,423,400 bp Quality-trimmed: 16,508,006 bp (0.6%) Total written (filtered): 2,587,883,920 bp (96.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10486555 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.5% C: 25.2% G: 16.0% T: 18.2% none/other: 5.1% Overview of removed sequences length count expect max.err error counts 1 7211785 6681058.5 0 7211785 2 1603420 1670264.6 0 1603420 3 502061 417566.2 0 502061 4 137281 104391.5 0 137281 5 51475 26097.9 0 51475 6 30001 6524.5 0 30001 7 26169 1631.1 0 26169 8 23638 407.8 0 23638 9 22327 101.9 0 21914 413 10 23967 25.5 1 20695 3272 11 19521 6.4 1 18461 1060 12 17758 1.6 1 16909 849 13 17054 0.4 1 16229 825 14 15600 0.4 1 14887 713 15 15199 0.4 1 14522 677 16 14210 0.4 1 13608 602 17 13475 0.4 1 12803 672 18 13394 0.4 1 12772 622 19 11958 0.4 1 11423 535 20 11038 0.4 1 10528 510 21 9903 0.4 1 9388 515 22 9158 0.4 1 8681 477 23 8508 0.4 1 8074 434 24 7687 0.4 1 7236 451 25 6887 0.4 1 6540 347 26 6856 0.4 1 6486 370 27 6493 0.4 1 6182 311 28 6337 0.4 1 6029 308 29 5722 0.4 1 5446 276 30 5394 0.4 1 5103 291 31 5275 0.4 1 5019 256 32 4901 0.4 1 4608 293 33 4533 0.4 1 4298 235 34 4291 0.4 1 4077 214 35 4136 0.4 1 3877 259 36 3741 0.4 1 3486 255 37 4071 0.4 1 3631 440 38 3129 0.4 1 2937 192 39 3089 0.4 1 2849 240 40 2942 0.4 1 2744 198 41 2573 0.4 1 2390 183 42 2110 0.4 1 1983 127 43 2890 0.4 1 2745 145 44 1162 0.4 1 1077 85 45 1723 0.4 1 1612 111 46 1679 0.4 1 1582 97 47 1905 0.4 1 1761 144 48 1874 0.4 1 1764 110 49 1901 0.4 1 1795 106 50 1771 0.4 1 1659 112 51 1864 0.4 1 1750 114 52 1731 0.4 1 1582 149 53 1535 0.4 1 1416 119 54 1339 0.4 1 1204 135 55 1347 0.4 1 1231 116 56 888 0.4 1 808 80 57 996 0.4 1 908 88 58 888 0.4 1 821 67 59 786 0.4 1 727 59 60 727 0.4 1 659 68 61 815 0.4 1 752 63 62 681 0.4 1 616 65 63 581 0.4 1 515 66 64 676 0.4 1 590 86 65 716 0.4 1 514 202 66 605 0.4 1 515 90 67 613 0.4 1 529 84 68 587 0.4 1 488 99 69 628 0.4 1 496 132 70 750 0.4 1 536 214 71 734 0.4 1 459 275 72 907 0.4 1 476 431 73 1510 0.4 1 504 1006 74 3436 0.4 1 529 2907 75 53016 0.4 1 777 52239 76 76935 0.4 1 1889 75046 77 73954 0.4 1 2706 71248 78 59704 0.4 1 2061 57643 79 35471 0.4 1 1514 33957 80 24120 0.4 1 1026 23094 81 15842 0.4 1 719 15123 82 10769 0.4 1 485 10284 83 6440 0.4 1 432 6008 84 4174 0.4 1 315 3859 85 3430 0.4 1 265 3165 86 2791 0.4 1 264 2527 87 2100 0.4 1 250 1850 88 1776 0.4 1 205 1571 89 1577 0.4 1 168 1409 90 1389 0.4 1 167 1222 91 1233 0.4 1 218 1015 92 1119 0.4 1 123 996 93 1196 0.4 1 99 1097 94 1438 0.4 1 94 1344 95 1639 0.4 1 114 1525 96 2274 0.4 1 108 2166 97 3385 0.4 1 228 3157 98 4572 0.4 1 130 4442 99 16559 0.4 1 162 16397 100 140340 0.4 1 501 139839 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz ============================================= 26724234 sequences processed in total