SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P06-GCCAAT-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-P06-GCCAAT-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 369.99 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 18,561,500 Reads with adapters: 6,834,093 (36.8%) Reads written (passing filters): 18,561,500 (100.0%) Total basepairs processed: 1,856,150,000 bp Quality-trimmed: 4,879,709 bp (0.3%) Total written (filtered): 1,828,627,143 bp (98.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6834093 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.6% C: 26.6% G: 16.1% T: 19.6% none/other: 2.0% Overview of removed sequences length count expect max.err error counts 1 5012807 4640375.0 0 5012807 2 1123453 1160093.8 0 1123453 3 334480 290023.4 0 334480 4 84832 72505.9 0 84832 5 24698 18126.5 0 24698 6 10272 4531.6 0 10272 7 7885 1132.9 0 7885 8 6908 283.2 0 6908 9 6843 70.8 0 6516 327 10 7837 17.7 1 5768 2069 11 5715 4.4 1 5196 519 12 5146 1.1 1 4880 266 13 4679 0.3 1 4438 241 14 4307 0.3 1 4093 214 15 3965 0.3 1 3790 175 16 3737 0.3 1 3555 182 17 3340 0.3 1 3149 191 18 3292 0.3 1 3106 186 19 2772 0.3 1 2635 137 20 2673 0.3 1 2487 186 21 2338 0.3 1 2201 137 22 2080 0.3 1 1961 119 23 1819 0.3 1 1733 86 24 1634 0.3 1 1522 112 25 1539 0.3 1 1446 93 26 1418 0.3 1 1346 72 27 1262 0.3 1 1189 73 28 1286 0.3 1 1192 94 29 1249 0.3 1 1167 82 30 1132 0.3 1 1075 57 31 1002 0.3 1 915 87 32 979 0.3 1 913 66 33 847 0.3 1 781 66 34 853 0.3 1 759 94 35 814 0.3 1 755 59 36 721 0.3 1 656 65 37 713 0.3 1 643 70 38 573 0.3 1 509 64 39 581 0.3 1 520 61 40 477 0.3 1 439 38 41 601 0.3 1 554 47 42 250 0.3 1 227 23 43 320 0.3 1 296 24 44 334 0.3 1 301 33 45 297 0.3 1 267 30 46 323 0.3 1 256 67 47 292 0.3 1 242 50 48 353 0.3 1 323 30 49 309 0.3 1 262 47 50 315 0.3 1 272 43 51 292 0.3 1 251 41 52 288 0.3 1 237 51 53 282 0.3 1 255 27 54 186 0.3 1 153 33 55 216 0.3 1 180 36 56 170 0.3 1 141 29 57 166 0.3 1 139 27 58 167 0.3 1 143 24 59 156 0.3 1 132 24 60 172 0.3 1 132 40 61 166 0.3 1 133 33 62 143 0.3 1 108 35 63 134 0.3 1 99 35 64 173 0.3 1 128 45 65 133 0.3 1 100 33 66 140 0.3 1 106 34 67 168 0.3 1 136 32 68 164 0.3 1 120 44 69 234 0.3 1 144 90 70 283 0.3 1 149 134 71 409 0.3 1 150 259 72 926 0.3 1 155 771 73 12487 0.3 1 166 12321 74 22317 0.3 1 498 21819 75 20727 0.3 1 718 20009 76 12784 0.3 1 551 12233 77 9024 0.3 1 422 8602 78 6155 0.3 1 261 5894 79 3908 0.3 1 225 3683 80 2907 0.3 1 152 2755 81 1945 0.3 1 115 1830 82 1287 0.3 1 79 1208 83 1076 0.3 1 101 975 84 858 0.3 1 100 758 85 650 0.3 1 88 562 86 519 0.3 1 81 438 87 431 0.3 1 73 358 88 356 0.3 1 35 321 89 305 0.3 1 63 242 90 278 0.3 1 49 229 91 286 0.3 1 52 234 92 293 0.3 1 36 257 93 292 0.3 1 22 270 94 371 0.3 1 28 343 95 447 0.3 1 40 407 96 568 0.3 1 22 546 97 883 0.3 1 59 824 98 1097 0.3 1 25 1072 99 4062 0.3 1 22 4040 100 36260 0.3 1 33 36227 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz ============================================= 18561500 sequences processed in total