SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P01-AGTTCC-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-P01-AGTTCC-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 498.41 s (20 us/read; 3.03 M reads/minute). === Summary === Total reads processed: 25,210,785 Reads with adapters: 9,194,471 (36.5%) Reads written (passing filters): 25,210,785 (100.0%) Total basepairs processed: 2,521,078,500 bp Quality-trimmed: 10,032,007 bp (0.4%) Total written (filtered): 2,474,313,959 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9194471 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.0% C: 27.3% G: 16.0% T: 19.0% none/other: 2.7% Overview of removed sequences length count expect max.err error counts 1 6684335 6302696.2 0 6684335 2 1479305 1575674.1 0 1479305 3 420317 393918.5 0 420317 4 107721 98479.6 0 107721 5 37827 24619.9 0 37827 6 18772 6155.0 0 18772 7 15295 1538.7 0 15295 8 13361 384.7 0 13361 9 12614 96.2 0 12295 319 10 15293 24.0 1 11451 3842 11 10854 6.0 1 9836 1018 12 9874 1.5 1 9142 732 13 9347 0.4 1 8555 792 14 8409 0.4 1 7721 688 15 8060 0.4 1 7425 635 16 7503 0.4 1 6897 606 17 7287 0.4 1 6700 587 18 6915 0.4 1 6370 545 19 5891 0.4 1 5429 462 20 5215 0.4 1 4762 453 21 4677 0.4 1 4288 389 22 4013 0.4 1 3645 368 23 3586 0.4 1 3253 333 24 3219 0.4 1 2937 282 25 3013 0.4 1 2761 252 26 2600 0.4 1 2382 218 27 2507 0.4 1 2269 238 28 2441 0.4 1 2221 220 29 2246 0.4 1 2032 214 30 2214 0.4 1 1995 219 31 1929 0.4 1 1717 212 32 1802 0.4 1 1619 183 33 1477 0.4 1 1346 131 34 1348 0.4 1 1214 134 35 1266 0.4 1 1112 154 36 1276 0.4 1 1106 170 37 1063 0.4 1 942 121 38 1074 0.4 1 964 110 39 936 0.4 1 808 128 40 788 0.4 1 692 96 41 721 0.4 1 640 81 42 588 0.4 1 511 77 43 791 0.4 1 695 96 44 326 0.4 1 284 42 45 529 0.4 1 469 60 46 499 0.4 1 426 73 47 483 0.4 1 397 86 48 499 0.4 1 423 76 49 446 0.4 1 370 76 50 389 0.4 1 312 77 51 389 0.4 1 334 55 52 325 0.4 1 270 55 53 278 0.4 1 232 46 54 283 0.4 1 225 58 55 292 0.4 1 249 43 56 173 0.4 1 141 32 57 204 0.4 1 148 56 58 185 0.4 1 148 37 59 181 0.4 1 138 43 60 151 0.4 1 124 27 61 167 0.4 1 134 33 62 129 0.4 1 92 37 63 157 0.4 1 121 36 64 157 0.4 1 124 33 65 156 0.4 1 102 54 66 118 0.4 1 86 32 67 173 0.4 1 131 42 68 170 0.4 1 123 47 69 183 0.4 1 125 58 70 229 0.4 1 138 91 71 264 0.4 1 159 105 72 345 0.4 1 129 216 73 612 0.4 1 122 490 74 1571 0.4 1 146 1425 75 27933 0.4 1 208 27725 76 36713 0.4 1 768 35945 77 33962 0.4 1 977 32985 78 26997 0.4 1 610 26387 79 15817 0.4 1 508 15309 80 10920 0.4 1 355 10565 81 7136 0.4 1 227 6909 82 4837 0.4 1 179 4658 83 2866 0.4 1 140 2726 84 1832 0.4 1 118 1714 85 1519 0.4 1 82 1437 86 1254 0.4 1 96 1158 87 975 0.4 1 106 869 88 738 0.4 1 75 663 89 713 0.4 1 63 650 90 550 0.4 1 60 490 91 568 0.4 1 79 489 92 477 0.4 1 51 426 93 551 0.4 1 43 508 94 651 0.4 1 37 614 95 848 0.4 1 66 782 96 1056 0.4 1 60 996 97 1512 0.4 1 117 1395 98 2112 0.4 1 51 2061 99 7505 0.4 1 27 7478 100 64596 0.4 1 46 64550 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz ============================================= 25210785 sequences processed in total