SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P12-TGACCA-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/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-P12-TGACCA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 555.02 s (21 us/read; 2.88 M reads/minute). === Summary === Total reads processed: 26,686,495 Reads with adapters: 10,347,910 (38.8%) Reads written (passing filters): 26,686,495 (100.0%) Total basepairs processed: 2,668,649,500 bp Quality-trimmed: 15,631,499 bp (0.6%) Total written (filtered): 2,622,269,897 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10347910 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.9% C: 23.7% G: 19.1% T: 18.0% none/other: 1.3% Overview of removed sequences length count expect max.err error counts 1 7315866 6671623.8 0 7315866 2 1852306 1667905.9 0 1852306 3 621196 416976.5 0 621196 4 152625 104244.1 0 152625 5 42728 26061.0 0 42728 6 17792 6515.3 0 17792 7 13674 1628.8 0 13674 8 11758 407.2 0 11758 9 12085 101.8 0 11412 673 10 11662 25.5 1 10008 1654 11 10451 6.4 1 9279 1172 12 9558 1.6 1 8764 794 13 8308 0.4 1 7840 468 14 9209 0.4 1 8560 649 15 6385 0.4 1 5983 402 16 6923 0.4 1 6482 441 17 8261 0.4 1 7697 564 18 4826 0.4 1 4530 296 19 6509 0.4 1 6008 501 20 4394 0.4 1 4115 279 21 4613 0.4 1 4295 318 22 4563 0.4 1 4147 416 23 4087 0.4 1 3661 426 24 3882 0.4 1 3498 384 25 3425 0.4 1 3116 309 26 3382 0.4 1 3042 340 27 3140 0.4 1 2848 292 28 2887 0.4 1 2596 291 29 2699 0.4 1 2385 314 30 3267 0.4 1 2900 367 31 2106 0.4 1 1886 220 32 2411 0.4 1 2143 268 33 2175 0.4 1 1907 268 34 2218 0.4 1 1947 271 35 2138 0.4 1 1856 282 36 2025 0.4 1 1744 281 37 1648 0.4 1 1446 202 38 1586 0.4 1 1317 269 39 1463 0.4 1 1281 182 40 1262 0.4 1 1106 156 41 1201 0.4 1 1026 175 42 1376 0.4 1 1179 197 43 809 0.4 1 697 112 44 1030 0.4 1 851 179 45 1236 0.4 1 987 249 46 737 0.4 1 605 132 47 769 0.4 1 629 140 48 1002 0.4 1 822 180 49 815 0.4 1 658 157 50 824 0.4 1 704 120 51 993 0.4 1 806 187 52 675 0.4 1 542 133 53 727 0.4 1 609 118 54 547 0.4 1 431 116 55 560 0.4 1 451 109 56 481 0.4 1 369 112 57 439 0.4 1 328 111 58 499 0.4 1 382 117 59 508 0.4 1 368 140 60 424 0.4 1 325 99 61 436 0.4 1 341 95 62 451 0.4 1 308 143 63 402 0.4 1 290 112 64 431 0.4 1 308 123 65 405 0.4 1 275 130 66 596 0.4 1 317 279 67 7367 0.4 1 335 7032 68 14539 0.4 1 956 13583 69 11969 0.4 1 1332 10637 70 9636 0.4 1 1108 8528 71 6161 0.4 1 776 5385 72 3468 0.4 1 547 2921 73 1815 0.4 1 368 1447 74 1215 0.4 1 220 995 75 820 0.4 1 198 622 76 533 0.4 1 146 387 77 501 0.4 1 166 335 78 437 0.4 1 88 349 79 461 0.4 1 168 293 80 386 0.4 1 124 262 81 311 0.4 1 103 208 82 276 0.4 1 104 172 83 372 0.4 1 126 246 84 335 0.4 1 130 205 85 323 0.4 1 122 201 86 316 0.4 1 117 199 87 343 0.4 1 133 210 88 364 0.4 1 150 214 89 306 0.4 1 73 233 90 332 0.4 1 65 267 91 478 0.4 1 112 366 92 405 0.4 1 54 351 93 490 0.4 1 48 442 94 785 0.4 1 51 734 95 1120 0.4 1 64 1056 96 1800 0.4 1 66 1734 97 2919 0.4 1 119 2800 98 4028 0.4 1 75 3953 99 11201 0.4 1 57 11144 100 62232 0.4 1 292 61940 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P12-TGACCA-READ2-Sequences.txt.gz ============================================= 26686495 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 26686495 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 221849 (0.83%)