SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P15-GTTTCG-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-P15-GTTTCG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 710.98 s (20 us/read; 2.95 M reads/minute). === Summary === Total reads processed: 34,898,106 Reads with adapters: 13,696,554 (39.2%) Reads written (passing filters): 34,898,106 (100.0%) Total basepairs processed: 3,489,810,600 bp Quality-trimmed: 16,415,739 bp (0.5%) Total written (filtered): 3,422,168,837 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13696554 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 23.3% G: 18.7% T: 18.3% none/other: 2.1% Overview of removed sequences length count expect max.err error counts 1 9508638 8724526.5 0 9508638 2 2388777 2181131.6 0 2388777 3 805242 545282.9 0 805242 4 206399 136320.7 0 206399 5 67746 34080.2 0 67746 6 34469 8520.0 0 34469 7 28973 2130.0 0 28973 8 25262 532.5 0 25262 9 24875 133.1 0 24119 756 10 24187 33.3 1 21782 2405 11 21083 8.3 1 19583 1500 12 19993 2.1 1 18884 1109 13 17334 0.5 1 16497 837 14 19446 0.5 1 18444 1002 15 13840 0.5 1 13188 652 16 14698 0.5 1 13992 706 17 16926 0.5 1 16105 821 18 10271 0.5 1 9773 498 19 13371 0.5 1 12709 662 20 9627 0.5 1 9163 464 21 9713 0.5 1 9246 467 22 8933 0.5 1 8348 585 23 8099 0.5 1 7498 601 24 7859 0.5 1 7380 479 25 6360 0.5 1 5947 413 26 6522 0.5 1 6100 422 27 6219 0.5 1 5808 411 28 5946 0.5 1 5583 363 29 5285 0.5 1 4910 375 30 5836 0.5 1 5432 404 31 3985 0.5 1 3710 275 32 4544 0.5 1 4233 311 33 4042 0.5 1 3741 301 34 3951 0.5 1 3655 296 35 3663 0.5 1 3377 286 36 3408 0.5 1 3137 271 37 2939 0.5 1 2701 238 38 2672 0.5 1 2439 233 39 2387 0.5 1 2162 225 40 2217 0.5 1 2030 187 41 2055 0.5 1 1808 247 42 2005 0.5 1 1813 192 43 1442 0.5 1 1289 153 44 1505 0.5 1 1344 161 45 1731 0.5 1 1517 214 46 1228 0.5 1 1044 184 47 1220 0.5 1 1063 157 48 1423 0.5 1 1265 158 49 1227 0.5 1 1089 138 50 1255 0.5 1 1086 169 51 1502 0.5 1 1297 205 52 937 0.5 1 815 122 53 949 0.5 1 808 141 54 842 0.5 1 720 122 55 753 0.5 1 622 131 56 673 0.5 1 565 108 57 607 0.5 1 495 112 58 554 0.5 1 458 96 59 481 0.5 1 371 110 60 454 0.5 1 371 83 61 438 0.5 1 350 88 62 440 0.5 1 330 110 63 383 0.5 1 279 104 64 454 0.5 1 317 137 65 464 0.5 1 285 179 66 741 0.5 1 278 463 67 18269 0.5 1 305 17964 68 21668 0.5 1 1344 20324 69 21419 0.5 1 1017 20402 70 21672 0.5 1 1043 20629 71 12349 0.5 1 1079 11270 72 8607 0.5 1 715 7892 73 6117 0.5 1 542 5575 74 3547 0.5 1 453 3094 75 2087 0.5 1 306 1781 76 1412 0.5 1 216 1196 77 1246 0.5 1 218 1028 78 908 0.5 1 168 740 79 744 0.5 1 171 573 80 690 0.5 1 132 558 81 601 0.5 1 153 448 82 515 0.5 1 115 400 83 560 0.5 1 151 409 84 468 0.5 1 109 359 85 454 0.5 1 144 310 86 444 0.5 1 123 321 87 483 0.5 1 150 333 88 546 0.5 1 152 394 89 511 0.5 1 111 400 90 557 0.5 1 98 459 91 743 0.5 1 131 612 92 675 0.5 1 73 602 93 756 0.5 1 43 713 94 1039 0.5 1 69 970 95 1568 0.5 1 67 1501 96 2481 0.5 1 81 2400 97 4175 0.5 1 146 4029 98 6009 0.5 1 85 5924 99 17494 0.5 1 37 17457 100 134240 0.5 1 103 134137 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P15-GTTTCG-READ2-Sequences.txt.gz ============================================= 34898106 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 34898106 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 365883 (1.05%)