SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P03-GTTTCG-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-P03-GTTTCG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 481.76 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 24,131,001 Reads with adapters: 8,357,907 (34.6%) Reads written (passing filters): 24,131,001 (100.0%) Total basepairs processed: 2,413,100,100 bp Quality-trimmed: 2,392,277 bp (0.1%) Total written (filtered): 2,390,213,755 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8357907 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.4% C: 30.5% G: 18.1% T: 17.5% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 6046725 6032750.2 0 6046725 2 1400491 1508187.6 0 1400491 3 396138 377046.9 0 396138 4 113373 94261.7 0 113373 5 45743 23565.4 0 45743 6 24829 5891.4 0 24829 7 21052 1472.8 0 21052 8 19047 368.2 0 19047 9 18123 92.1 0 17719 404 10 19383 23.0 1 16127 3256 11 15485 5.8 1 14692 793 12 14277 1.4 1 13528 749 13 13474 0.4 1 12840 634 14 12138 0.4 1 11553 585 15 11888 0.4 1 11295 593 16 10797 0.4 1 10299 498 17 10117 0.4 1 9577 540 18 9597 0.4 1 9096 501 19 8314 0.4 1 7856 458 20 7704 0.4 1 7345 359 21 6753 0.4 1 6402 351 22 6224 0.4 1 5895 329 23 5442 0.4 1 5156 286 24 5067 0.4 1 4805 262 25 4670 0.4 1 4436 234 26 4257 0.4 1 4047 210 27 4004 0.4 1 3768 236 28 3934 0.4 1 3761 173 29 3455 0.4 1 3281 174 30 3530 0.4 1 3356 174 31 3005 0.4 1 2845 160 32 2803 0.4 1 2659 144 33 2589 0.4 1 2442 147 34 2392 0.4 1 2269 123 35 2151 0.4 1 2045 106 36 2102 0.4 1 1985 117 37 1883 0.4 1 1764 119 38 1688 0.4 1 1595 93 39 1525 0.4 1 1433 92 40 1349 0.4 1 1257 92 41 1288 0.4 1 1203 85 42 1016 0.4 1 937 79 43 1384 0.4 1 1308 76 44 498 0.4 1 448 50 45 761 0.4 1 701 60 46 743 0.4 1 680 63 47 770 0.4 1 695 75 48 795 0.4 1 723 72 49 747 0.4 1 702 45 50 735 0.4 1 676 59 51 703 0.4 1 636 67 52 610 0.4 1 555 55 53 563 0.4 1 518 45 54 450 0.4 1 399 51 55 559 0.4 1 508 51 56 325 0.4 1 282 43 57 333 0.4 1 297 36 58 299 0.4 1 273 26 59 309 0.4 1 256 53 60 375 0.4 1 322 53 61 243 0.4 1 209 34 62 313 0.4 1 268 45 63 301 0.4 1 260 41 64 284 0.4 1 236 48 65 306 0.4 1 260 46 66 321 0.4 1 278 43 67 273 0.4 1 238 35 68 321 0.4 1 280 41 69 331 0.4 1 301 30 70 362 0.4 1 314 48 71 324 0.4 1 263 61 72 371 0.4 1 316 55 73 476 0.4 1 372 104 74 671 0.4 1 403 268 75 4074 0.4 1 512 3562 76 7316 0.4 1 2154 5162 77 7527 0.4 1 2588 4939 78 5742 0.4 1 1923 3819 79 4134 0.4 1 1489 2645 80 2772 0.4 1 992 1780 81 1847 0.4 1 725 1122 82 1224 0.4 1 486 738 83 865 0.4 1 383 482 84 611 0.4 1 308 303 85 548 0.4 1 316 232 86 522 0.4 1 312 210 87 427 0.4 1 267 160 88 413 0.4 1 292 121 89 353 0.4 1 245 108 90 257 0.4 1 170 87 91 324 0.4 1 230 94 92 235 0.4 1 149 86 93 237 0.4 1 142 95 94 234 0.4 1 126 108 95 318 0.4 1 182 136 96 388 0.4 1 217 171 97 577 0.4 1 308 269 98 505 0.4 1 193 312 99 1174 0.4 1 84 1090 100 9605 0.4 1 112 9493 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P03-GTTTCG-READ1-Sequences.txt.gz ============================================= 24131001 sequences processed in total