SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-ACTGAT-READ2-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-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 846.41 s (20 us/read; 2.93 M reads/minute). === Summary === Total reads processed: 41,291,102 Reads with adapters: 15,949,282 (38.6%) Reads written (passing filters): 41,291,102 (100.0%) Total basepairs processed: 4,129,110,200 bp Quality-trimmed: 26,563,539 bp (0.6%) Total written (filtered): 4,061,473,467 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15949282 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.4% C: 25.0% G: 19.3% T: 16.4% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 11409600 10322775.5 0 11409600 2 2844816 2580693.9 0 2844816 3 954024 645173.5 0 954024 4 232577 161293.4 0 232577 5 60175 40323.3 0 60175 6 24185 10080.8 0 24185 7 17749 2520.2 0 17749 8 15256 630.1 0 15256 9 15638 157.5 0 14245 1393 10 15667 39.4 1 12825 2842 11 13801 9.8 1 11786 2015 12 12355 2.5 1 11189 1166 13 10677 0.6 1 9777 900 14 11542 0.6 1 10627 915 15 8533 0.6 1 7938 595 16 9044 0.6 1 8374 670 17 10263 0.6 1 9448 815 18 6243 0.6 1 5717 526 19 8129 0.6 1 7442 687 20 5948 0.6 1 5478 470 21 5911 0.6 1 5444 467 22 5545 0.6 1 5071 474 23 5142 0.6 1 4670 472 24 5136 0.6 1 4567 569 25 4235 0.6 1 3864 371 26 4201 0.6 1 3772 429 27 3803 0.6 1 3435 368 28 3733 0.6 1 3382 351 29 3428 0.6 1 3129 299 30 3757 0.6 1 3380 377 31 2606 0.6 1 2380 226 32 3018 0.6 1 2708 310 33 2628 0.6 1 2372 256 34 2650 0.6 1 2390 260 35 2283 0.6 1 1993 290 36 2461 0.6 1 2162 299 37 2072 0.6 1 1857 215 38 2014 0.6 1 1754 260 39 1797 0.6 1 1583 214 40 1589 0.6 1 1363 226 41 1531 0.6 1 1272 259 42 1687 0.6 1 1455 232 43 1101 0.6 1 935 166 44 1286 0.6 1 1023 263 45 1525 0.6 1 1266 259 46 979 0.6 1 841 138 47 979 0.6 1 831 148 48 1254 0.6 1 1046 208 49 953 0.6 1 805 148 50 990 0.6 1 825 165 51 1247 0.6 1 1042 205 52 796 0.6 1 645 151 53 756 0.6 1 626 130 54 723 0.6 1 566 157 55 673 0.6 1 531 142 56 597 0.6 1 453 144 57 602 0.6 1 471 131 58 551 0.6 1 405 146 59 540 0.6 1 413 127 60 589 0.6 1 437 152 61 543 0.6 1 384 159 62 647 0.6 1 449 198 63 602 0.6 1 386 216 64 549 0.6 1 376 173 65 624 0.6 1 403 221 66 921 0.6 1 473 448 67 10088 0.6 1 380 9708 68 14447 0.6 1 1558 12889 69 14085 0.6 1 1226 12859 70 12334 0.6 1 1288 11046 71 9232 0.6 1 1185 8047 72 6389 0.6 1 911 5478 73 4760 0.6 1 714 4046 74 3065 0.6 1 607 2458 75 1955 0.6 1 445 1510 76 1434 0.6 1 323 1111 77 1282 0.6 1 297 985 78 951 0.6 1 245 706 79 716 0.6 1 184 532 80 709 0.6 1 218 491 81 633 0.6 1 241 392 82 558 0.6 1 197 361 83 550 0.6 1 198 352 84 521 0.6 1 202 319 85 487 0.6 1 182 305 86 484 0.6 1 229 255 87 491 0.6 1 185 306 88 512 0.6 1 199 313 89 467 0.6 1 154 313 90 447 0.6 1 107 340 91 555 0.6 1 167 388 92 455 0.6 1 67 388 93 534 0.6 1 58 476 94 616 0.6 1 58 558 95 943 0.6 1 102 841 96 1344 0.6 1 88 1256 97 2163 0.6 1 166 1997 98 2976 0.6 1 101 2875 99 8821 0.6 1 62 8759 100 66802 0.6 1 262 66540 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-ACTGAT-READ2-Sequences.txt.gz ============================================= 41291102 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 41291102 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 314461 (0.76%)