SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P03-ACTGAT-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-P03-ACTGAT-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 471.27 s (20 us/read; 2.96 M reads/minute). === Summary === Total reads processed: 23,215,719 Reads with adapters: 8,971,997 (38.6%) Reads written (passing filters): 23,215,719 (100.0%) Total basepairs processed: 2,321,571,900 bp Quality-trimmed: 14,419,093 bp (0.6%) Total written (filtered): 2,281,293,686 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8971997 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.7% C: 24.4% G: 19.2% T: 17.6% none/other: 1.2% Overview of removed sequences length count expect max.err error counts 1 6335931 5803929.8 0 6335931 2 1617726 1450982.4 0 1617726 3 535354 362745.6 0 535354 4 131792 90686.4 0 131792 5 36956 22671.6 0 36956 6 16035 5667.9 0 16035 7 11931 1417.0 0 11931 8 10462 354.2 0 10462 9 10644 88.6 0 9963 681 10 10404 22.1 1 8782 1622 11 9157 5.5 1 8086 1071 12 8484 1.4 1 7728 756 13 7358 0.3 1 6838 520 14 8168 0.3 1 7594 574 15 5862 0.3 1 5442 420 16 6195 0.3 1 5803 392 17 7310 0.3 1 6805 505 18 4569 0.3 1 4247 322 19 5715 0.3 1 5281 434 20 4085 0.3 1 3782 303 21 4292 0.3 1 3978 314 22 3930 0.3 1 3594 336 23 3812 0.3 1 3452 360 24 3703 0.3 1 3333 370 25 3016 0.3 1 2714 302 26 3034 0.3 1 2710 324 27 2854 0.3 1 2591 263 28 2915 0.3 1 2603 312 29 2604 0.3 1 2320 284 30 2978 0.3 1 2661 317 31 1898 0.3 1 1684 214 32 2196 0.3 1 1955 241 33 2003 0.3 1 1756 247 34 2122 0.3 1 1850 272 35 2017 0.3 1 1751 266 36 1960 0.3 1 1721 239 37 1641 0.3 1 1426 215 38 1651 0.3 1 1417 234 39 1442 0.3 1 1247 195 40 1303 0.3 1 1147 156 41 1317 0.3 1 1136 181 42 1363 0.3 1 1149 214 43 930 0.3 1 785 145 44 1011 0.3 1 834 177 45 1207 0.3 1 1003 204 46 832 0.3 1 659 173 47 905 0.3 1 767 138 48 996 0.3 1 837 159 49 843 0.3 1 704 139 50 879 0.3 1 744 135 51 1120 0.3 1 925 195 52 635 0.3 1 494 141 53 690 0.3 1 564 126 54 598 0.3 1 496 102 55 627 0.3 1 504 123 56 537 0.3 1 421 116 57 563 0.3 1 418 145 58 472 0.3 1 371 101 59 477 0.3 1 375 102 60 448 0.3 1 350 98 61 464 0.3 1 378 86 62 451 0.3 1 323 128 63 451 0.3 1 329 122 64 413 0.3 1 298 115 65 423 0.3 1 291 132 66 555 0.3 1 339 216 67 6522 0.3 1 337 6185 68 8691 0.3 1 1063 7628 69 9191 0.3 1 870 8321 70 9190 0.3 1 984 8206 71 5771 0.3 1 869 4902 72 4258 0.3 1 639 3619 73 3111 0.3 1 497 2614 74 1985 0.3 1 432 1553 75 1261 0.3 1 305 956 76 873 0.3 1 207 666 77 770 0.3 1 204 566 78 637 0.3 1 147 490 79 529 0.3 1 157 372 80 507 0.3 1 135 372 81 406 0.3 1 135 271 82 440 0.3 1 139 301 83 458 0.3 1 157 301 84 359 0.3 1 137 222 85 296 0.3 1 113 183 86 307 0.3 1 104 203 87 350 0.3 1 131 219 88 292 0.3 1 106 186 89 305 0.3 1 74 231 90 318 0.3 1 65 253 91 393 0.3 1 77 316 92 306 0.3 1 50 256 93 369 0.3 1 30 339 94 427 0.3 1 31 396 95 574 0.3 1 37 537 96 885 0.3 1 56 829 97 1573 0.3 1 115 1458 98 2118 0.3 1 66 2052 99 5906 0.3 1 22 5884 100 47903 0.3 1 64 47839 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz ============================================= 23215719 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 23215719 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 190733 (0.82%)