SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P13-ATCACG-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-P13-ATCACG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 362.52 s (20 us/read; 2.94 M reads/minute). === Summary === Total reads processed: 17,735,907 Reads with adapters: 6,970,945 (39.3%) Reads written (passing filters): 17,735,907 (100.0%) Total basepairs processed: 1,773,590,700 bp Quality-trimmed: 15,221,319 bp (0.9%) Total written (filtered): 1,712,687,846 bp (96.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6970945 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.3% C: 20.7% G: 18.4% T: 17.9% none/other: 5.8% Overview of removed sequences length count expect max.err error counts 1 4746186 4433976.8 0 4746186 2 1142863 1108494.2 0 1142863 3 392446 277123.5 0 392446 4 95516 69280.9 0 95516 5 28992 17320.2 0 28992 6 14655 4330.1 0 14655 7 11335 1082.5 0 11335 8 9910 270.6 0 9910 9 9936 67.7 0 9570 366 10 9287 16.9 1 8333 954 11 8520 4.2 1 7877 643 12 7715 1.1 1 7268 447 13 6860 0.3 1 6506 354 14 7704 0.3 1 7287 417 15 5367 0.3 1 5110 257 16 5726 0.3 1 5405 321 17 6678 0.3 1 6287 391 18 3964 0.3 1 3757 207 19 5257 0.3 1 4972 285 20 3599 0.3 1 3377 222 21 3720 0.3 1 3506 214 22 3214 0.3 1 2997 217 23 2953 0.3 1 2782 171 24 2870 0.3 1 2703 167 25 2582 0.3 1 2407 175 26 2358 0.3 1 2207 151 27 2210 0.3 1 2051 159 28 2124 0.3 1 2001 123 29 1829 0.3 1 1711 118 30 2052 0.3 1 1919 133 31 1343 0.3 1 1246 97 32 1461 0.3 1 1342 119 33 1297 0.3 1 1173 124 34 1346 0.3 1 1250 96 35 1046 0.3 1 961 85 36 1052 0.3 1 983 69 37 958 0.3 1 888 70 38 877 0.3 1 790 87 39 867 0.3 1 800 67 40 708 0.3 1 647 61 41 620 0.3 1 538 82 42 591 0.3 1 529 62 43 427 0.3 1 392 35 44 428 0.3 1 394 34 45 474 0.3 1 411 63 46 347 0.3 1 304 43 47 335 0.3 1 287 48 48 346 0.3 1 309 37 49 363 0.3 1 314 49 50 348 0.3 1 297 51 51 399 0.3 1 347 52 52 239 0.3 1 183 56 53 252 0.3 1 220 32 54 198 0.3 1 154 44 55 195 0.3 1 174 21 56 181 0.3 1 150 31 57 149 0.3 1 123 26 58 155 0.3 1 126 29 59 129 0.3 1 90 39 60 147 0.3 1 108 39 61 162 0.3 1 128 34 62 128 0.3 1 89 39 63 141 0.3 1 98 43 64 155 0.3 1 91 64 65 215 0.3 1 83 132 66 603 0.3 1 74 529 67 26660 0.3 1 92 26568 68 43423 0.3 1 334 43089 69 41446 0.3 1 537 40909 70 33636 0.3 1 381 33255 71 19663 0.3 1 288 19375 72 11661 0.3 1 211 11450 73 6845 0.3 1 138 6707 74 3976 0.3 1 85 3891 75 2724 0.3 1 96 2628 76 1658 0.3 1 43 1615 77 1696 0.3 1 61 1635 78 1640 0.3 1 31 1609 79 1305 0.3 1 74 1231 80 1195 0.3 1 45 1150 81 976 0.3 1 42 934 82 870 0.3 1 46 824 83 769 0.3 1 54 715 84 655 0.3 1 36 619 85 601 0.3 1 43 558 86 609 0.3 1 44 565 87 605 0.3 1 49 556 88 639 0.3 1 43 596 89 698 0.3 1 14 684 90 719 0.3 1 25 694 91 837 0.3 1 32 805 92 925 0.3 1 24 901 93 1127 0.3 1 18 1109 94 1634 0.3 1 12 1622 95 2461 0.3 1 18 2443 96 3480 0.3 1 15 3465 97 5469 0.3 1 23 5446 98 8104 0.3 1 22 8082 99 21514 0.3 1 29 21485 100 153615 0.3 1 79 153536 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz ============================================= 17735907 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17735907 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 450424 (2.54%)