SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P04-ATCACG-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-P04-ATCACG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 481.58 s (20 us/read; 2.98 M reads/minute). === Summary === Total reads processed: 23,947,263 Reads with adapters: 8,995,189 (37.6%) Reads written (passing filters): 23,947,263 (100.0%) Total basepairs processed: 2,394,726,300 bp Quality-trimmed: 8,132,265 bp (0.3%) Total written (filtered): 2,337,222,912 bp (97.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8995189 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.5% C: 27.8% G: 16.5% T: 17.3% none/other: 3.9% Overview of removed sequences length count expect max.err error counts 1 6480105 5986815.8 0 6480105 2 1323326 1496703.9 0 1323326 3 410673 374176.0 0 410673 4 109970 93544.0 0 109970 5 38792 23386.0 0 38792 6 20710 5846.5 0 20710 7 17210 1461.6 0 17210 8 15287 365.4 0 15287 9 15337 91.4 0 14996 341 10 16535 22.8 1 12567 3968 11 13341 5.7 1 12356 985 12 11944 1.4 1 11093 851 13 10737 0.4 1 10035 702 14 10692 0.4 1 9951 741 15 9350 0.4 1 8734 616 16 9481 0.4 1 8784 697 17 8721 0.4 1 8068 653 18 8613 0.4 1 7936 677 19 7324 0.4 1 6802 522 20 6449 0.4 1 5978 471 21 6234 0.4 1 5762 472 22 5363 0.4 1 4957 406 23 4871 0.4 1 4516 355 24 4707 0.4 1 4329 378 25 4179 0.4 1 3885 294 26 4009 0.4 1 3742 267 27 3706 0.4 1 3443 263 28 3622 0.4 1 3390 232 29 3488 0.4 1 3189 299 30 3096 0.4 1 2873 223 31 2967 0.4 1 2784 183 32 2526 0.4 1 2356 170 33 2629 0.4 1 2419 210 34 2325 0.4 1 2137 188 35 2361 0.4 1 2184 177 36 2017 0.4 1 1869 148 37 1947 0.4 1 1785 162 38 1835 0.4 1 1654 181 39 1566 0.4 1 1430 136 40 1450 0.4 1 1326 124 41 2327 0.4 1 2133 194 42 459 0.4 1 405 54 43 685 0.4 1 625 60 44 831 0.4 1 771 60 45 874 0.4 1 793 81 46 854 0.4 1 775 79 47 835 0.4 1 767 68 48 867 0.4 1 781 86 49 920 0.4 1 825 95 50 813 0.4 1 731 82 51 746 0.4 1 676 70 52 672 0.4 1 605 67 53 709 0.4 1 630 79 54 495 0.4 1 432 63 55 425 0.4 1 376 49 56 359 0.4 1 305 54 57 397 0.4 1 350 47 58 373 0.4 1 312 61 59 318 0.4 1 270 48 60 302 0.4 1 255 47 61 307 0.4 1 262 45 62 316 0.4 1 260 56 63 334 0.4 1 256 78 64 290 0.4 1 229 61 65 281 0.4 1 239 42 66 325 0.4 1 253 72 67 290 0.4 1 213 77 68 359 0.4 1 246 113 69 398 0.4 1 269 129 70 466 0.4 1 258 208 71 660 0.4 1 266 394 72 1264 0.4 1 306 958 73 14199 0.4 1 330 13869 74 18698 0.4 1 786 17912 75 15198 0.4 1 893 14305 76 12888 0.4 1 793 12095 77 11259 0.4 1 806 10453 78 9357 0.4 1 632 8725 79 8405 0.4 1 642 7763 80 7695 0.4 1 625 7070 81 6477 0.4 1 565 5912 82 5526 0.4 1 555 4971 83 5234 0.4 1 487 4747 84 4986 0.4 1 550 4436 85 4440 0.4 1 508 3932 86 4069 0.4 1 507 3562 87 3943 0.4 1 401 3542 88 3485 0.4 1 453 3032 89 3208 0.4 1 390 2818 90 3024 0.4 1 302 2722 91 3159 0.4 1 394 2765 92 3003 0.4 1 213 2790 93 3098 0.4 1 234 2864 94 3651 0.4 1 199 3452 95 4170 0.4 1 237 3933 96 5263 0.4 1 336 4927 97 7405 0.4 1 438 6967 98 9258 0.4 1 223 9035 99 22870 0.4 1 144 22726 100 162175 0.4 1 164 162011 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P04-ATCACG-READ1-Sequences.txt.gz ============================================= 23947263 sequences processed in total