SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P03-ACTGAT-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-P03-ACTGAT-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 460.43 s (20 us/read; 3.03 M reads/minute). === Summary === Total reads processed: 23,215,719 Reads with adapters: 8,194,852 (35.3%) Reads written (passing filters): 23,215,719 (100.0%) Total basepairs processed: 2,321,571,900 bp Quality-trimmed: 5,207,744 bp (0.2%) Total written (filtered): 2,292,790,871 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8194852 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.6% C: 28.5% G: 16.5% T: 19.2% none/other: 1.3% Overview of removed sequences length count expect max.err error counts 1 6038992 5803929.8 0 6038992 2 1352531 1450982.4 0 1352531 3 379888 362745.6 0 379888 4 97837 90686.4 0 97837 5 31884 22671.6 0 31884 6 14491 5667.9 0 14491 7 11346 1417.0 0 11346 8 10207 354.2 0 10207 9 9872 88.6 0 9494 378 10 10524 22.1 1 8528 1996 11 8358 5.5 1 7760 598 12 7763 1.4 1 7297 466 13 7288 0.3 1 6847 441 14 6636 0.3 1 6272 364 15 6517 0.3 1 6143 374 16 6035 0.3 1 5741 294 17 5754 0.3 1 5469 285 18 5542 0.3 1 5220 322 19 4796 0.3 1 4557 239 20 4421 0.3 1 4156 265 21 4150 0.3 1 3875 275 22 3675 0.3 1 3448 227 23 3405 0.3 1 3197 208 24 3108 0.3 1 2926 182 25 2867 0.3 1 2705 162 26 2654 0.3 1 2502 152 27 2554 0.3 1 2380 174 28 2503 0.3 1 2347 156 29 2337 0.3 1 2189 148 30 2215 0.3 1 2064 151 31 1968 0.3 1 1857 111 32 1898 0.3 1 1766 132 33 1703 0.3 1 1606 97 34 1818 0.3 1 1699 119 35 1567 0.3 1 1441 126 36 1595 0.3 1 1457 138 37 1399 0.3 1 1272 127 38 1386 0.3 1 1285 101 39 1241 0.3 1 1148 93 40 1096 0.3 1 1019 77 41 1067 0.3 1 976 91 42 863 0.3 1 803 60 43 1117 0.3 1 1044 73 44 476 0.3 1 427 49 45 650 0.3 1 594 56 46 673 0.3 1 625 48 47 750 0.3 1 687 63 48 730 0.3 1 668 62 49 690 0.3 1 635 55 50 698 0.3 1 643 55 51 651 0.3 1 590 61 52 496 0.3 1 445 51 53 532 0.3 1 472 60 54 490 0.3 1 431 59 55 447 0.3 1 399 48 56 316 0.3 1 277 39 57 336 0.3 1 300 36 58 293 0.3 1 247 46 59 309 0.3 1 268 41 60 286 0.3 1 249 37 61 268 0.3 1 238 30 62 228 0.3 1 197 31 63 258 0.3 1 223 35 64 233 0.3 1 197 36 65 240 0.3 1 202 38 66 260 0.3 1 223 37 67 227 0.3 1 200 27 68 238 0.3 1 185 53 69 261 0.3 1 218 43 70 290 0.3 1 241 49 71 294 0.3 1 228 66 72 338 0.3 1 216 122 73 448 0.3 1 243 205 74 732 0.3 1 286 446 75 8248 0.3 1 346 7902 76 13400 0.3 1 917 12483 77 14730 0.3 1 1375 13355 78 12864 0.3 1 1066 11798 79 8187 0.3 1 984 7203 80 5871 0.3 1 637 5234 81 3977 0.3 1 469 3508 82 2808 0.3 1 327 2481 83 1759 0.3 1 301 1458 84 1233 0.3 1 213 1020 85 992 0.3 1 176 816 86 862 0.3 1 201 661 87 608 0.3 1 167 441 88 499 0.3 1 117 382 89 433 0.3 1 122 311 90 408 0.3 1 114 294 91 371 0.3 1 133 238 92 341 0.3 1 94 247 93 328 0.3 1 83 245 94 392 0.3 1 65 327 95 418 0.3 1 75 343 96 560 0.3 1 78 482 97 851 0.3 1 146 705 98 1042 0.3 1 78 964 99 3418 0.3 1 43 3375 100 28246 0.3 1 60 28186 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz ============================================= 23215719 sequences processed in total