SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P07-AGTCAA-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-P07-AGTCAA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 512.32 s (20 us/read; 3.05 M reads/minute). === Summary === Total reads processed: 26,060,601 Reads with adapters: 9,261,389 (35.5%) Reads written (passing filters): 26,060,601 (100.0%) Total basepairs processed: 2,606,060,100 bp Quality-trimmed: 3,634,254 bp (0.1%) Total written (filtered): 2,578,109,104 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9261389 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.1% C: 28.9% G: 16.5% T: 19.6% none/other: 1.0% Overview of removed sequences length count expect max.err error counts 1 6795262 6515150.2 0 6795262 2 1528861 1628787.6 0 1528861 3 438293 407196.9 0 438293 4 114850 101799.2 0 114850 5 41277 25449.8 0 41277 6 21398 6362.5 0 21398 7 17389 1590.6 0 17389 8 15815 397.7 0 15815 9 15057 99.4 0 14743 314 10 15852 24.9 1 13323 2529 11 12604 6.2 1 11900 704 12 11601 1.6 1 11150 451 13 10563 0.4 1 10152 411 14 9939 0.4 1 9547 392 15 9466 0.4 1 9098 368 16 8644 0.4 1 8295 349 17 8087 0.4 1 7804 283 18 7872 0.4 1 7557 315 19 6588 0.4 1 6333 255 20 6207 0.4 1 5972 235 21 5659 0.4 1 5409 250 22 4768 0.4 1 4554 214 23 4485 0.4 1 4313 172 24 4070 0.4 1 3871 199 25 3728 0.4 1 3560 168 26 3427 0.4 1 3274 153 27 3380 0.4 1 3240 140 28 3044 0.4 1 2900 144 29 2907 0.4 1 2778 129 30 2713 0.4 1 2604 109 31 2514 0.4 1 2417 97 32 2334 0.4 1 2201 133 33 2041 0.4 1 1966 75 34 1938 0.4 1 1832 106 35 1746 0.4 1 1654 92 36 1742 0.4 1 1647 95 37 1495 0.4 1 1406 89 38 1380 0.4 1 1297 83 39 1154 0.4 1 1093 61 40 1012 0.4 1 959 53 41 1016 0.4 1 952 64 42 956 0.4 1 889 67 43 1199 0.4 1 1141 58 44 420 0.4 1 388 32 45 575 0.4 1 541 34 46 573 0.4 1 539 34 47 612 0.4 1 576 36 48 603 0.4 1 560 43 49 552 0.4 1 517 35 50 546 0.4 1 508 38 51 471 0.4 1 431 40 52 465 0.4 1 422 43 53 444 0.4 1 407 37 54 363 0.4 1 330 33 55 387 0.4 1 341 46 56 276 0.4 1 252 24 57 269 0.4 1 246 23 58 242 0.4 1 208 34 59 229 0.4 1 203 26 60 246 0.4 1 228 18 61 195 0.4 1 175 20 62 207 0.4 1 177 30 63 162 0.4 1 141 21 64 196 0.4 1 170 26 65 192 0.4 1 151 41 66 193 0.4 1 157 36 67 216 0.4 1 191 25 68 200 0.4 1 175 25 69 215 0.4 1 181 34 70 230 0.4 1 181 49 71 262 0.4 1 195 67 72 267 0.4 1 186 81 73 356 0.4 1 203 153 74 628 0.4 1 219 409 75 8379 0.4 1 349 8030 76 11849 0.4 1 986 10863 77 12578 0.4 1 1301 11277 78 11049 0.4 1 1085 9964 79 6939 0.4 1 922 6017 80 4870 0.4 1 673 4197 81 3362 0.4 1 441 2921 82 2313 0.4 1 364 1949 83 1392 0.4 1 279 1113 84 886 0.4 1 212 674 85 784 0.4 1 186 598 86 653 0.4 1 192 461 87 537 0.4 1 176 361 88 443 0.4 1 150 293 89 368 0.4 1 107 261 90 328 0.4 1 132 196 91 331 0.4 1 132 199 92 271 0.4 1 92 179 93 291 0.4 1 95 196 94 319 0.4 1 82 237 95 397 0.4 1 101 296 96 491 0.4 1 97 394 97 720 0.4 1 181 539 98 828 0.4 1 90 738 99 2815 0.4 1 59 2756 100 23071 0.4 1 65 23006 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz ============================================= 26060601 sequences processed in total