SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-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/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-P08-ACTGAT-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 804.99 s (19 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 41,291,102 Reads with adapters: 14,466,467 (35.0%) Reads written (passing filters): 41,291,102 (100.0%) Total basepairs processed: 4,129,110,200 bp Quality-trimmed: 8,835,488 bp (0.2%) Total written (filtered): 4,082,776,233 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14466467 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.9% C: 29.0% G: 16.8% T: 18.2% none/other: 1.1% Overview of removed sequences length count expect max.err error counts 1 10798854 10322775.5 0 10798854 2 2340224 2580693.9 0 2340224 3 662545 645173.5 0 662545 4 179322 161293.4 0 179322 5 56519 40323.3 0 56519 6 24042 10080.8 0 24042 7 17791 2520.2 0 17791 8 15095 630.1 0 15095 9 14800 157.5 0 14092 708 10 18454 39.4 1 12727 5727 11 12641 9.8 1 11705 936 12 11495 2.5 1 10846 649 13 10513 0.6 1 9978 535 14 9674 0.6 1 9183 491 15 9494 0.6 1 8998 496 16 8869 0.6 1 8377 492 17 8198 0.6 1 7733 465 18 7595 0.6 1 7185 410 19 7070 0.6 1 6691 379 20 6406 0.6 1 6067 339 21 5767 0.6 1 5438 329 22 5221 0.6 1 4922 299 23 4670 0.6 1 4399 271 24 4459 0.6 1 4205 254 25 4041 0.6 1 3814 227 26 3799 0.6 1 3620 179 27 3379 0.6 1 3182 197 28 3302 0.6 1 3139 163 29 3150 0.6 1 2992 158 30 2832 0.6 1 2677 155 31 2750 0.6 1 2587 163 32 2657 0.6 1 2499 158 33 2392 0.6 1 2261 131 34 2292 0.6 1 2135 157 35 1859 0.6 1 1735 124 36 2052 0.6 1 1879 173 37 1767 0.6 1 1651 116 38 1703 0.6 1 1599 104 39 1515 0.6 1 1428 87 40 1329 0.6 1 1235 94 41 1236 0.6 1 1112 124 42 1076 0.6 1 991 85 43 1307 0.6 1 1247 60 44 639 0.6 1 566 73 45 853 0.6 1 777 76 46 799 0.6 1 741 58 47 810 0.6 1 741 69 48 861 0.6 1 789 72 49 741 0.6 1 676 65 50 751 0.6 1 687 64 51 715 0.6 1 644 71 52 647 0.6 1 574 73 53 572 0.6 1 500 72 54 523 0.6 1 436 87 55 477 0.6 1 405 72 56 325 0.6 1 266 59 57 378 0.6 1 330 48 58 292 0.6 1 254 38 59 362 0.6 1 302 60 60 331 0.6 1 281 50 61 251 0.6 1 213 38 62 320 0.6 1 268 52 63 242 0.6 1 204 38 64 266 0.6 1 212 54 65 323 0.6 1 242 81 66 366 0.6 1 324 42 67 265 0.6 1 208 57 68 293 0.6 1 239 54 69 311 0.6 1 241 70 70 283 0.6 1 192 91 71 340 0.6 1 250 90 72 430 0.6 1 289 141 73 535 0.6 1 294 241 74 1071 0.6 1 394 677 75 11032 0.6 1 448 10584 76 20217 0.6 1 1415 18802 77 21589 0.6 1 2189 19400 78 17912 0.6 1 1769 16143 79 12905 0.6 1 1404 11501 80 9087 0.6 1 1001 8086 81 6011 0.6 1 739 5272 82 4239 0.6 1 553 3686 83 2735 0.6 1 449 2286 84 1935 0.6 1 365 1570 85 1581 0.6 1 358 1223 86 1353 0.6 1 325 1028 87 926 0.6 1 282 644 88 860 0.6 1 266 594 89 720 0.6 1 212 508 90 530 0.6 1 148 382 91 636 0.6 1 252 384 92 493 0.6 1 116 377 93 500 0.6 1 126 374 94 508 0.6 1 117 391 95 698 0.6 1 154 544 96 943 0.6 1 149 794 97 1335 0.6 1 297 1038 98 1615 0.6 1 142 1473 99 5106 0.6 1 81 5025 100 41473 0.6 1 237 41236 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-ACTGAT-READ1-Sequences.txt.gz ============================================= 41291102 sequences processed in total