SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P06-AGTTCC-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-P06-AGTTCC-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 786.98 s (19 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 40,368,134 Reads with adapters: 14,197,828 (35.2%) Reads written (passing filters): 40,368,134 (100.0%) Total basepairs processed: 4,036,813,400 bp Quality-trimmed: 7,044,525 bp (0.2%) Total written (filtered): 3,997,473,804 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14197828 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.0% C: 29.2% G: 17.0% T: 18.2% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 10581222 10092033.5 0 10581222 2 2315314 2523008.4 0 2315314 3 663415 630752.1 0 663415 4 177609 157688.0 0 177609 5 58613 39422.0 0 58613 6 25998 9855.5 0 25998 7 20258 2463.9 0 20258 8 17506 616.0 0 17506 9 17598 154.0 0 16936 662 10 21029 38.5 1 14927 6102 11 14552 9.6 1 13493 1059 12 13783 2.4 1 12865 918 13 12466 0.6 1 11585 881 14 11604 0.6 1 10822 782 15 11216 0.6 1 10496 720 16 10153 0.6 1 9416 737 17 9714 0.6 1 9001 713 18 9290 0.6 1 8639 651 19 7857 0.6 1 7305 552 20 7529 0.6 1 7020 509 21 6848 0.6 1 6374 474 22 6054 0.6 1 5623 431 23 5334 0.6 1 4963 371 24 4815 0.6 1 4508 307 25 4543 0.6 1 4238 305 26 4188 0.6 1 3915 273 27 4065 0.6 1 3794 271 28 3740 0.6 1 3482 258 29 3396 0.6 1 3183 213 30 3312 0.6 1 3068 244 31 3208 0.6 1 2991 217 32 2986 0.6 1 2785 201 33 2503 0.6 1 2318 185 34 2366 0.6 1 2186 180 35 2168 0.6 1 1996 172 36 2151 0.6 1 1950 201 37 1793 0.6 1 1658 135 38 1758 0.6 1 1593 165 39 1558 0.6 1 1427 131 40 1394 0.6 1 1284 110 41 1470 0.6 1 1351 119 42 1097 0.6 1 985 112 43 1360 0.6 1 1245 115 44 609 0.6 1 550 59 45 745 0.6 1 673 72 46 826 0.6 1 768 58 47 847 0.6 1 760 87 48 820 0.6 1 743 77 49 808 0.6 1 719 89 50 673 0.6 1 602 71 51 655 0.6 1 567 88 52 646 0.6 1 567 79 53 567 0.6 1 488 79 54 510 0.6 1 427 83 55 494 0.6 1 421 73 56 363 0.6 1 291 72 57 427 0.6 1 355 72 58 354 0.6 1 285 69 59 356 0.6 1 278 78 60 325 0.6 1 255 70 61 265 0.6 1 222 43 62 301 0.6 1 255 46 63 268 0.6 1 227 41 64 305 0.6 1 260 45 65 348 0.6 1 294 54 66 371 0.6 1 305 66 67 283 0.6 1 221 62 68 325 0.6 1 261 64 69 437 0.6 1 364 73 70 379 0.6 1 311 68 71 444 0.6 1 342 102 72 480 0.6 1 352 128 73 611 0.6 1 411 200 74 1078 0.6 1 507 571 75 9212 0.6 1 610 8602 76 15026 0.6 1 2443 12583 77 14492 0.6 1 3193 11299 78 10468 0.6 1 2153 8315 79 7506 0.6 1 1794 5712 80 4931 0.6 1 1208 3723 81 3112 0.6 1 799 2313 82 2267 0.6 1 607 1660 83 1488 0.6 1 473 1015 84 1055 0.6 1 378 677 85 889 0.6 1 367 522 86 832 0.6 1 398 434 87 641 0.6 1 318 323 88 610 0.6 1 334 276 89 517 0.6 1 282 235 90 411 0.6 1 225 186 91 500 0.6 1 297 203 92 388 0.6 1 189 199 93 338 0.6 1 160 178 94 370 0.6 1 158 212 95 521 0.6 1 236 285 96 674 0.6 1 307 367 97 896 0.6 1 350 546 98 942 0.6 1 186 756 99 2641 0.6 1 105 2536 100 22348 0.6 1 123 22225 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P06-AGTTCC-READ1-Sequences.txt.gz ============================================= 40368134 sequences processed in total