SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P10-GTCCGC-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-P10-GTCCGC-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 318.82 s (20 us/read; 3.00 M reads/minute). === Summary === Total reads processed: 15,948,623 Reads with adapters: 5,973,336 (37.5%) Reads written (passing filters): 15,948,623 (100.0%) Total basepairs processed: 1,594,862,300 bp Quality-trimmed: 6,386,037 bp (0.4%) Total written (filtered): 1,563,092,833 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5973336 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.6% C: 27.6% G: 16.2% T: 17.7% none/other: 2.8% Overview of removed sequences length count expect max.err error counts 1 4310177 3987155.8 0 4310177 2 915859 996788.9 0 915859 3 273741 249197.2 0 273741 4 77220 62299.3 0 77220 5 27851 15574.8 0 27851 6 15238 3893.7 0 15238 7 12990 973.4 0 12990 8 11310 243.4 0 11310 9 10871 60.8 0 10652 219 10 13718 15.2 1 9962 3756 11 9263 3.8 1 8726 537 12 8850 1.0 1 8446 404 13 8333 0.2 1 7942 391 14 7461 0.2 1 7097 364 15 7374 0.2 1 7040 334 16 6780 0.2 1 6456 324 17 6653 0.2 1 6318 335 18 6351 0.2 1 6058 293 19 5481 0.2 1 5196 285 20 5097 0.2 1 4828 269 21 4636 0.2 1 4381 255 22 4284 0.2 1 4080 204 23 3845 0.2 1 3671 174 24 3629 0.2 1 3470 159 25 3394 0.2 1 3242 152 26 3116 0.2 1 2975 141 27 2914 0.2 1 2789 125 28 2908 0.2 1 2784 124 29 2611 0.2 1 2472 139 30 2586 0.2 1 2470 116 31 2286 0.2 1 2195 91 32 2109 0.2 1 2014 95 33 1945 0.2 1 1842 103 34 1815 0.2 1 1703 112 35 1789 0.2 1 1699 90 36 1614 0.2 1 1533 81 37 1561 0.2 1 1456 105 38 1358 0.2 1 1287 71 39 1259 0.2 1 1185 74 40 1296 0.2 1 1230 66 41 1040 0.2 1 977 63 42 1026 0.2 1 967 59 43 1116 0.2 1 1066 50 44 480 0.2 1 456 24 45 667 0.2 1 635 32 46 665 0.2 1 632 33 47 736 0.2 1 692 44 48 663 0.2 1 632 31 49 596 0.2 1 569 27 50 579 0.2 1 557 22 51 532 0.2 1 500 32 52 576 0.2 1 540 36 53 459 0.2 1 425 34 54 398 0.2 1 358 40 55 383 0.2 1 355 28 56 268 0.2 1 232 36 57 237 0.2 1 222 15 58 218 0.2 1 205 13 59 185 0.2 1 159 26 60 152 0.2 1 127 25 61 140 0.2 1 119 21 62 136 0.2 1 118 18 63 114 0.2 1 101 13 64 120 0.2 1 97 23 65 127 0.2 1 93 34 66 99 0.2 1 71 28 67 118 0.2 1 81 37 68 101 0.2 1 69 32 69 110 0.2 1 62 48 70 136 0.2 1 79 57 71 147 0.2 1 69 78 72 241 0.2 1 73 168 73 410 0.2 1 92 318 74 1126 0.2 1 108 1018 75 15462 0.2 1 126 15336 76 25873 0.2 1 494 25379 77 22790 0.2 1 696 22094 78 16494 0.2 1 490 16004 79 11155 0.2 1 349 10806 80 7590 0.2 1 261 7329 81 4716 0.2 1 160 4556 82 3221 0.2 1 133 3088 83 1997 0.2 1 103 1894 84 1297 0.2 1 72 1225 85 1097 0.2 1 76 1021 86 812 0.2 1 66 746 87 610 0.2 1 60 550 88 521 0.2 1 61 460 89 446 0.2 1 43 403 90 398 0.2 1 55 343 91 363 0.2 1 46 317 92 388 0.2 1 30 358 93 368 0.2 1 31 337 94 418 0.2 1 31 387 95 542 0.2 1 34 508 96 737 0.2 1 75 662 97 1030 0.2 1 79 951 98 1379 0.2 1 50 1329 99 5015 0.2 1 27 4988 100 42943 0.2 1 51 42892 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P10-GTCCGC-READ1-Sequences.txt.gz ============================================= 15948623 sequences processed in total