SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P09-GGCTAC-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-P09-GGCTAC-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 701.02 s (21 us/read; 2.88 M reads/minute). === Summary === Total reads processed: 33,663,894 Reads with adapters: 13,005,017 (38.6%) Reads written (passing filters): 33,663,894 (100.0%) Total basepairs processed: 3,366,389,400 bp Quality-trimmed: 21,365,391 bp (0.6%) Total written (filtered): 3,303,948,874 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13005017 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.8% C: 24.8% G: 19.7% T: 16.2% none/other: 1.5% Overview of removed sequences length count expect max.err error counts 1 9108829 8415973.5 0 9108829 2 2316172 2103993.4 0 2316172 3 766665 525998.3 0 766665 4 198067 131499.6 0 198067 5 60042 32874.9 0 60042 6 29619 8218.7 0 29619 7 23677 2054.7 0 23677 8 20423 513.7 0 20423 9 20647 128.4 0 19528 1119 10 19726 32.1 1 17430 2296 11 17391 8.0 1 15620 1771 12 16340 2.0 1 15141 1199 13 14099 0.5 1 13100 999 14 16189 0.5 1 14949 1240 15 10852 0.5 1 10069 783 16 11923 0.5 1 11080 843 17 14236 0.5 1 13164 1072 18 8017 0.5 1 7382 635 19 11045 0.5 1 10245 800 20 7575 0.5 1 7052 523 21 8210 0.5 1 7663 547 22 7538 0.5 1 7048 490 23 6825 0.5 1 6349 476 24 6604 0.5 1 6146 458 25 5460 0.5 1 5075 385 26 5378 0.5 1 5004 374 27 5235 0.5 1 4868 367 28 4940 0.5 1 4593 347 29 4328 0.5 1 4037 291 30 5120 0.5 1 4776 344 31 3378 0.5 1 3153 225 32 3759 0.5 1 3494 265 33 3156 0.5 1 2941 215 34 3255 0.5 1 3018 237 35 2830 0.5 1 2636 194 36 2907 0.5 1 2648 259 37 2563 0.5 1 2357 206 38 2387 0.5 1 2182 205 39 2103 0.5 1 1933 170 40 1894 0.5 1 1739 155 41 1685 0.5 1 1521 164 42 1724 0.5 1 1544 180 43 1067 0.5 1 971 96 44 1290 0.5 1 1145 145 45 1500 0.5 1 1320 180 46 908 0.5 1 808 100 47 1110 0.5 1 993 117 48 1207 0.5 1 1074 133 49 1121 0.5 1 982 139 50 993 0.5 1 880 113 51 1130 0.5 1 971 159 52 716 0.5 1 642 74 53 776 0.5 1 671 105 54 653 0.5 1 547 106 55 585 0.5 1 498 87 56 489 0.5 1 381 108 57 448 0.5 1 372 76 58 389 0.5 1 297 92 59 388 0.5 1 299 89 60 364 0.5 1 288 76 61 353 0.5 1 267 86 62 346 0.5 1 238 108 63 302 0.5 1 207 95 64 279 0.5 1 157 122 65 381 0.5 1 184 197 66 689 0.5 1 169 520 67 13440 0.5 1 166 13274 68 25135 0.5 1 624 24511 69 17842 0.5 1 856 16986 70 11984 0.5 1 634 11350 71 8375 0.5 1 436 7939 72 4517 0.5 1 333 4184 73 2198 0.5 1 194 2004 74 1482 0.5 1 139 1343 75 940 0.5 1 107 833 76 694 0.5 1 100 594 77 545 0.5 1 68 477 78 533 0.5 1 75 458 79 486 0.5 1 80 406 80 400 0.5 1 69 331 81 406 0.5 1 81 325 82 416 0.5 1 83 333 83 325 0.5 1 82 243 84 329 0.5 1 98 231 85 334 0.5 1 96 238 86 286 0.5 1 80 206 87 323 0.5 1 74 249 88 379 0.5 1 84 295 89 355 0.5 1 69 286 90 404 0.5 1 40 364 91 466 0.5 1 61 405 92 487 0.5 1 56 431 93 712 0.5 1 31 681 94 1015 0.5 1 25 990 95 1634 0.5 1 42 1592 96 2499 0.5 1 38 2461 97 3983 0.5 1 97 3886 98 5247 0.5 1 48 5199 99 14678 0.5 1 12 14666 100 81871 0.5 1 54 81817 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P09-GGCTAC-READ2-Sequences.txt.gz ============================================= 33663894 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 33663894 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 311472 (0.93%)