SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P04-GTCCGC-READ2-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-P04-GTCCGC-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 470.70 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 22,919,563 Reads with adapters: 9,218,728 (40.2%) Reads written (passing filters): 22,919,563 (100.0%) Total basepairs processed: 2,291,956,300 bp Quality-trimmed: 15,523,382 bp (0.7%) Total written (filtered): 2,227,595,137 bp (97.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9218728 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 22.9% G: 18.5% T: 17.3% none/other: 3.7% Overview of removed sequences length count expect max.err error counts 1 6258815 5729890.8 0 6258815 2 1545045 1432472.7 0 1545045 3 525991 358118.2 0 525991 4 138997 89529.5 0 138997 5 47732 22382.4 0 47732 6 26936 5595.6 0 26936 7 23445 1398.9 0 23445 8 20708 349.7 0 20708 9 20126 87.4 0 19533 593 10 19305 21.9 1 17652 1653 11 16687 5.5 1 15581 1106 12 16127 1.4 1 15236 891 13 13989 0.3 1 13319 670 14 16093 0.3 1 15217 876 15 11058 0.3 1 10440 618 16 12056 0.3 1 11382 674 17 14565 0.3 1 13726 839 18 8105 0.3 1 7702 403 19 11272 0.3 1 10682 590 20 7605 0.3 1 7224 381 21 7917 0.3 1 7498 419 22 7347 0.3 1 6881 466 23 6564 0.3 1 6145 419 24 6535 0.3 1 6110 425 25 5287 0.3 1 4992 295 26 5247 0.3 1 4970 277 27 5181 0.3 1 4861 320 28 4859 0.3 1 4536 323 29 4455 0.3 1 4154 301 30 4918 0.3 1 4621 297 31 3319 0.3 1 3097 222 32 3833 0.3 1 3559 274 33 3318 0.3 1 3082 236 34 3203 0.3 1 2996 207 35 2881 0.3 1 2687 194 36 3043 0.3 1 2850 193 37 2667 0.3 1 2521 146 38 2366 0.3 1 2146 220 39 2198 0.3 1 2037 161 40 1969 0.3 1 1847 122 41 1846 0.3 1 1667 179 42 1826 0.3 1 1673 153 43 1273 0.3 1 1174 99 44 1377 0.3 1 1234 143 45 1496 0.3 1 1334 162 46 1133 0.3 1 992 141 47 1169 0.3 1 1063 106 48 1361 0.3 1 1246 115 49 1251 0.3 1 1129 122 50 1135 0.3 1 1036 99 51 1275 0.3 1 1150 125 52 955 0.3 1 834 121 53 912 0.3 1 810 102 54 834 0.3 1 767 67 55 717 0.3 1 631 86 56 670 0.3 1 584 86 57 580 0.3 1 486 94 58 559 0.3 1 479 80 59 489 0.3 1 414 75 60 479 0.3 1 403 76 61 525 0.3 1 460 65 62 444 0.3 1 342 102 63 450 0.3 1 355 95 64 427 0.3 1 316 111 65 511 0.3 1 320 191 66 986 0.3 1 293 693 67 25220 0.3 1 290 24930 68 27258 0.3 1 1560 25698 69 26824 0.3 1 1034 25790 70 27054 0.3 1 1202 25852 71 13895 0.3 1 1132 12763 72 9185 0.3 1 674 8511 73 6446 0.3 1 490 5956 74 3349 0.3 1 361 2988 75 1929 0.3 1 268 1661 76 1330 0.3 1 161 1169 77 1121 0.3 1 196 925 78 859 0.3 1 154 705 79 730 0.3 1 155 575 80 700 0.3 1 146 554 81 559 0.3 1 141 418 82 528 0.3 1 134 394 83 628 0.3 1 136 492 84 459 0.3 1 135 324 85 464 0.3 1 120 344 86 397 0.3 1 101 296 87 464 0.3 1 106 358 88 503 0.3 1 123 380 89 504 0.3 1 86 418 90 590 0.3 1 106 484 91 748 0.3 1 112 636 92 681 0.3 1 54 627 93 835 0.3 1 43 792 94 1115 0.3 1 33 1082 95 1769 0.3 1 56 1713 96 2800 0.3 1 58 2742 97 4825 0.3 1 127 4698 98 7416 0.3 1 78 7338 99 20601 0.3 1 28 20573 100 160498 0.3 1 103 160395 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P04-GTCCGC-READ2-Sequences.txt.gz ============================================= 22919563 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 22919563 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 422713 (1.84%)