SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P10-GTCCGC-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-P10-GTCCGC-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 329.92 s (21 us/read; 2.90 M reads/minute). === Summary === Total reads processed: 15,948,623 Reads with adapters: 6,249,122 (39.2%) Reads written (passing filters): 15,948,623 (100.0%) Total basepairs processed: 1,594,862,300 bp Quality-trimmed: 9,243,325 bp (0.6%) Total written (filtered): 1,559,262,090 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6249122 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.9% C: 23.7% G: 18.8% T: 17.0% none/other: 2.6% Overview of removed sequences length count expect max.err error counts 1 4344226 3987155.8 0 4344226 2 1064741 996788.9 0 1064741 3 349312 249197.2 0 349312 4 93068 62299.3 0 93068 5 28995 15574.8 0 28995 6 15949 3893.7 0 15949 7 13122 973.4 0 13122 8 11250 243.4 0 11250 9 11385 60.8 0 10850 535 10 11029 15.2 1 9893 1136 11 9569 3.8 1 8766 803 12 9211 1.0 1 8570 641 13 8050 0.2 1 7547 503 14 8810 0.2 1 8177 633 15 6357 0.2 1 5833 524 16 6890 0.2 1 6295 595 17 8096 0.2 1 7534 562 18 4746 0.2 1 4430 316 19 6278 0.2 1 5877 401 20 4355 0.2 1 4070 285 21 4635 0.2 1 4302 333 22 4299 0.2 1 4045 254 23 3970 0.2 1 3678 292 24 3820 0.2 1 3571 249 25 3279 0.2 1 3080 199 26 3195 0.2 1 2975 220 27 2997 0.2 1 2785 212 28 3003 0.2 1 2828 175 29 2594 0.2 1 2445 149 30 3014 0.2 1 2808 206 31 1959 0.2 1 1838 121 32 2234 0.2 1 2051 183 33 1888 0.2 1 1769 119 34 1894 0.2 1 1780 114 35 1801 0.2 1 1691 110 36 1698 0.2 1 1586 112 37 1566 0.2 1 1436 130 38 1367 0.2 1 1294 73 39 1285 0.2 1 1189 96 40 1237 0.2 1 1159 78 41 1097 0.2 1 1005 92 42 1120 0.2 1 1020 100 43 726 0.2 1 666 60 44 806 0.2 1 728 78 45 919 0.2 1 823 96 46 623 0.2 1 566 57 47 724 0.2 1 656 68 48 715 0.2 1 645 70 49 616 0.2 1 565 51 50 629 0.2 1 543 86 51 690 0.2 1 620 70 52 509 0.2 1 459 50 53 474 0.2 1 434 40 54 405 0.2 1 351 54 55 368 0.2 1 316 52 56 311 0.2 1 274 37 57 263 0.2 1 220 43 58 263 0.2 1 218 45 59 206 0.2 1 170 36 60 188 0.2 1 130 58 61 173 0.2 1 138 35 62 205 0.2 1 127 78 63 171 0.2 1 120 51 64 173 0.2 1 108 65 65 194 0.2 1 103 91 66 577 0.2 1 87 490 67 13081 0.2 1 94 12987 68 14017 0.2 1 482 13535 69 13328 0.2 1 309 13019 70 11766 0.2 1 369 11397 71 7010 0.2 1 354 6656 72 4398 0.2 1 194 4204 73 2985 0.2 1 152 2833 74 1646 0.2 1 128 1518 75 901 0.2 1 92 809 76 687 0.2 1 34 653 77 545 0.2 1 53 492 78 382 0.2 1 45 337 79 313 0.2 1 44 269 80 328 0.2 1 40 288 81 269 0.2 1 42 227 82 267 0.2 1 59 208 83 256 0.2 1 46 210 84 189 0.2 1 52 137 85 226 0.2 1 46 180 86 216 0.2 1 57 159 87 204 0.2 1 39 165 88 243 0.2 1 40 203 89 213 0.2 1 31 182 90 282 0.2 1 35 247 91 362 0.2 1 42 320 92 319 0.2 1 23 296 93 380 0.2 1 9 371 94 539 0.2 1 18 521 95 856 0.2 1 24 832 96 1375 0.2 1 22 1353 97 2267 0.2 1 49 2218 98 3499 0.2 1 35 3464 99 10070 0.2 1 12 10058 100 75384 0.2 1 52 75332 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P10-GTCCGC-READ2-Sequences.txt.gz ============================================= 15948623 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 15948623 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 208889 (1.31%)