SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P11-GAGTGG-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/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-P11-GAGTGG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 888.17 s (20 us/read; 2.94 M reads/minute). === Summary === Total reads processed: 43,493,444 Reads with adapters: 16,796,875 (38.6%) Reads written (passing filters): 43,493,444 (100.0%) Total basepairs processed: 4,349,344,400 bp Quality-trimmed: 26,974,785 bp (0.6%) Total written (filtered): 4,242,203,063 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16796875 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.8% C: 25.1% G: 17.3% T: 17.6% none/other: 3.2% Overview of removed sequences length count expect max.err error counts 1 11825709 10873361.0 0 11825709 2 2653755 2718340.2 0 2653755 3 865963 679585.1 0 865963 4 239563 169896.3 0 239563 5 82090 42474.1 0 82090 6 44447 10618.5 0 44447 7 37036 2654.6 0 37036 8 32402 663.7 0 32402 9 31466 165.9 0 30440 1026 10 32286 41.5 1 27697 4589 11 26907 10.4 1 24842 2065 12 25780 2.6 1 24027 1753 13 22891 0.6 1 21350 1541 14 24511 0.6 1 22922 1589 15 18488 0.6 1 17172 1316 16 19023 0.6 1 17697 1326 17 21527 0.6 1 20138 1389 18 14000 0.6 1 13073 927 19 17308 0.6 1 16187 1121 20 13178 0.6 1 12167 1011 21 13188 0.6 1 12403 785 22 11950 0.6 1 11199 751 23 11203 0.6 1 10442 761 24 10516 0.6 1 9784 732 25 9071 0.6 1 8519 552 26 8821 0.6 1 8318 503 27 8502 0.6 1 7920 582 28 7923 0.6 1 7473 450 29 7231 0.6 1 6817 414 30 7992 0.6 1 7472 520 31 5772 0.6 1 5426 346 32 6229 0.6 1 5876 353 33 5484 0.6 1 5110 374 34 5564 0.6 1 5231 333 35 5127 0.6 1 4847 280 36 4977 0.6 1 4664 313 37 4591 0.6 1 4292 299 38 4398 0.6 1 4150 248 39 3688 0.6 1 3451 237 40 3316 0.6 1 3099 217 41 3302 0.6 1 3023 279 42 3144 0.6 1 2895 249 43 2274 0.6 1 2101 173 44 2345 0.6 1 2141 204 45 2848 0.6 1 2630 218 46 2010 0.6 1 1842 168 47 2272 0.6 1 2084 188 48 2447 0.6 1 2234 213 49 2238 0.6 1 2086 152 50 2168 0.6 1 1973 195 51 2534 0.6 1 2311 223 52 1820 0.6 1 1654 166 53 1845 0.6 1 1674 171 54 1675 0.6 1 1501 174 55 1509 0.6 1 1342 167 56 1406 0.6 1 1242 164 57 1207 0.6 1 1081 126 58 1197 0.6 1 1046 151 59 1101 0.6 1 962 139 60 1035 0.6 1 913 122 61 925 0.6 1 820 105 62 958 0.6 1 813 145 63 846 0.6 1 711 135 64 932 0.6 1 705 227 65 1003 0.6 1 677 326 66 1706 0.6 1 654 1052 67 35096 0.6 1 646 34450 68 44350 0.6 1 2372 41978 69 42845 0.6 1 2038 40807 70 38389 0.6 1 2132 36257 71 26130 0.6 1 2012 24118 72 17842 0.6 1 1436 16406 73 12888 0.6 1 1237 11651 74 7530 0.6 1 853 6677 75 4429 0.6 1 583 3846 76 3028 0.6 1 391 2637 77 2583 0.6 1 361 2222 78 1879 0.6 1 316 1563 79 1488 0.6 1 256 1232 80 1487 0.6 1 300 1187 81 1212 0.6 1 319 893 82 1107 0.6 1 296 811 83 1048 0.6 1 266 782 84 877 0.6 1 209 668 85 805 0.6 1 212 593 86 852 0.6 1 235 617 87 900 0.6 1 207 693 88 970 0.6 1 194 776 89 947 0.6 1 172 775 90 985 0.6 1 136 849 91 1220 0.6 1 164 1056 92 1171 0.6 1 75 1096 93 1333 0.6 1 78 1255 94 1775 0.6 1 45 1730 95 2647 0.6 1 71 2576 96 4225 0.6 1 67 4158 97 7382 0.6 1 147 7235 98 10747 0.6 1 99 10648 99 32475 0.6 1 196 32279 100 243613 0.6 1 320 243293 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P11-GAGTGG-READ2-Sequences.txt.gz ============================================= 43493444 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 43493444 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 675001 (1.55%)