SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P12-TGACCA-READ1-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-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 522.50 s (20 us/read; 3.06 M reads/minute). === Summary === Total reads processed: 26,686,495 Reads with adapters: 9,470,009 (35.5%) Reads written (passing filters): 26,686,495 (100.0%) Total basepairs processed: 2,668,649,500 bp Quality-trimmed: 6,856,366 bp (0.3%) Total written (filtered): 2,633,995,216 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9470009 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.6% C: 28.1% G: 16.3% T: 19.5% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 6983865 6671623.8 0 6983865 2 1555501 1667905.9 0 1555501 3 438779 416976.5 0 438779 4 111942 104244.1 0 111942 5 36171 26061.0 0 36171 6 16604 6515.3 0 16604 7 13077 1628.8 0 13077 8 11630 407.2 0 11630 9 11180 101.8 0 10956 224 10 12166 25.5 1 9856 2310 11 9658 6.4 1 9013 645 12 8771 1.6 1 8348 423 13 8370 0.4 1 7958 412 14 7482 0.4 1 7146 336 15 7346 0.4 1 7013 333 16 6690 0.4 1 6383 307 17 6450 0.4 1 6153 297 18 6111 0.4 1 5829 282 19 5450 0.4 1 5194 256 20 4892 0.4 1 4674 218 21 4448 0.4 1 4236 212 22 4255 0.4 1 4039 216 23 3565 0.4 1 3411 154 24 3280 0.4 1 3111 169 25 3313 0.4 1 3146 167 26 2971 0.4 1 2825 146 27 2788 0.4 1 2654 134 28 2517 0.4 1 2369 148 29 2423 0.4 1 2274 149 30 2414 0.4 1 2280 134 31 2205 0.4 1 2090 115 32 2060 0.4 1 1933 127 33 1902 0.4 1 1797 105 34 1859 0.4 1 1737 122 35 1736 0.4 1 1634 102 36 1637 0.4 1 1515 122 37 1354 0.4 1 1273 81 38 1273 0.4 1 1178 95 39 1301 0.4 1 1155 146 40 1097 0.4 1 1012 85 41 1331 0.4 1 1238 93 42 568 0.4 1 522 46 43 684 0.4 1 642 42 44 680 0.4 1 625 55 45 691 0.4 1 629 62 46 664 0.4 1 586 78 47 642 0.4 1 575 67 48 716 0.4 1 648 68 49 661 0.4 1 594 67 50 683 0.4 1 611 72 51 598 0.4 1 543 55 52 559 0.4 1 493 66 53 566 0.4 1 501 65 54 357 0.4 1 295 62 55 374 0.4 1 327 47 56 302 0.4 1 272 30 57 286 0.4 1 240 46 58 303 0.4 1 261 42 59 244 0.4 1 206 38 60 326 0.4 1 217 109 61 318 0.4 1 230 88 62 267 0.4 1 200 67 63 240 0.4 1 177 63 64 275 0.4 1 214 61 65 209 0.4 1 169 40 66 232 0.4 1 189 43 67 260 0.4 1 206 54 68 215 0.4 1 170 45 69 310 0.4 1 206 104 70 398 0.4 1 241 157 71 438 0.4 1 201 237 72 964 0.4 1 208 756 73 13649 0.4 1 319 13330 74 21479 0.4 1 1145 20334 75 20199 0.4 1 1469 18730 76 13212 0.4 1 1198 12014 77 9485 0.4 1 915 8570 78 6338 0.4 1 642 5696 79 4184 0.4 1 501 3683 80 3106 0.4 1 300 2806 81 2003 0.4 1 233 1770 82 1357 0.4 1 161 1196 83 1188 0.4 1 189 999 84 966 0.4 1 198 768 85 661 0.4 1 170 491 86 576 0.4 1 138 438 87 544 0.4 1 187 357 88 459 0.4 1 165 294 89 337 0.4 1 79 258 90 325 0.4 1 84 241 91 371 0.4 1 118 253 92 292 0.4 1 62 230 93 328 0.4 1 61 267 94 395 0.4 1 59 336 95 408 0.4 1 64 344 96 643 0.4 1 94 549 97 947 0.4 1 167 780 98 1177 0.4 1 83 1094 99 4067 0.4 1 67 4000 100 35419 0.4 1 157 35262 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P12-TGACCA-READ1-Sequences.txt.gz ============================================= 26686495 sequences processed in total