SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P02-CTTGTA-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-P02-CTTGTA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 677.31 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 33,011,434 Reads with adapters: 12,613,343 (38.2%) Reads written (passing filters): 33,011,434 (100.0%) Total basepairs processed: 3,301,143,400 bp Quality-trimmed: 16,379,164 bp (0.5%) Total written (filtered): 3,253,695,574 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12613343 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.7% C: 25.1% G: 19.6% T: 16.9% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 8968608 8252858.5 0 8968608 2 2281900 2063214.6 0 2281900 3 754405 515803.7 0 754405 4 187723 128950.9 0 187723 5 51807 32237.7 0 51807 6 22408 8059.4 0 22408 7 17526 2014.9 0 17526 8 15105 503.7 0 15105 9 15296 125.9 0 14213 1083 10 15091 31.5 1 12918 2173 11 12877 7.9 1 11332 1545 12 11759 2.0 1 10707 1052 13 10188 0.5 1 9397 791 14 11526 0.5 1 10692 834 15 8099 0.5 1 7395 704 16 8764 0.5 1 8098 666 17 9847 0.5 1 8992 855 18 6058 0.5 1 5583 475 19 7897 0.5 1 7244 653 20 5358 0.5 1 4898 460 21 5505 0.5 1 5050 455 22 4975 0.5 1 4586 389 23 4640 0.5 1 4242 398 24 4501 0.5 1 4067 434 25 3655 0.5 1 3353 302 26 3679 0.5 1 3370 309 27 3481 0.5 1 3185 296 28 3359 0.5 1 3061 298 29 3101 0.5 1 2831 270 30 3410 0.5 1 3068 342 31 2314 0.5 1 2098 216 32 2590 0.5 1 2318 272 33 2253 0.5 1 2047 206 34 2214 0.5 1 1965 249 35 1894 0.5 1 1691 203 36 2021 0.5 1 1762 259 37 1770 0.5 1 1571 199 38 1638 0.5 1 1418 220 39 1489 0.5 1 1328 161 40 1360 0.5 1 1177 183 41 1312 0.5 1 1138 174 42 1328 0.5 1 1138 190 43 803 0.5 1 691 112 44 981 0.5 1 819 162 45 1289 0.5 1 1058 231 46 787 0.5 1 624 163 47 827 0.5 1 701 126 48 942 0.5 1 788 154 49 777 0.5 1 661 116 50 804 0.5 1 678 126 51 1020 0.5 1 821 199 52 594 0.5 1 491 103 53 661 0.5 1 522 139 54 601 0.5 1 488 113 55 610 0.5 1 486 124 56 542 0.5 1 420 122 57 492 0.5 1 390 102 58 505 0.5 1 385 120 59 516 0.5 1 383 133 60 456 0.5 1 345 111 61 504 0.5 1 374 130 62 477 0.5 1 337 140 63 472 0.5 1 360 112 64 509 0.5 1 343 166 65 536 0.5 1 363 173 66 671 0.5 1 385 286 67 5487 0.5 1 410 5077 68 11649 0.5 1 1733 9916 69 10444 0.5 1 2382 8062 70 7884 0.5 1 1938 5946 71 5775 0.5 1 1498 4277 72 3636 0.5 1 1116 2520 73 2031 0.5 1 679 1352 74 1277 0.5 1 391 886 75 896 0.5 1 308 588 76 620 0.5 1 261 359 77 621 0.5 1 246 375 78 526 0.5 1 181 345 79 495 0.5 1 229 266 80 488 0.5 1 256 232 81 447 0.5 1 222 225 82 444 0.5 1 232 212 83 395 0.5 1 221 174 84 436 0.5 1 236 200 85 486 0.5 1 257 229 86 440 0.5 1 259 181 87 392 0.5 1 185 207 88 545 0.5 1 306 239 89 470 0.5 1 197 273 90 377 0.5 1 119 258 91 535 0.5 1 192 343 92 420 0.5 1 115 305 93 480 0.5 1 113 367 94 657 0.5 1 92 565 95 981 0.5 1 143 838 96 1472 0.5 1 151 1321 97 2345 0.5 1 283 2062 98 2701 0.5 1 119 2582 99 6909 0.5 1 49 6860 100 39475 0.5 1 105 39370 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P02-CTTGTA-READ2-Sequences.txt.gz ============================================= 33011434 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 33011434 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 199835 (0.61%)