SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P07-ATGTCA-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/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-P07-ATGTCA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 570.19 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 29,165,404 Reads with adapters: 10,188,517 (34.9%) Reads written (passing filters): 29,165,404 (100.0%) Total basepairs processed: 2,916,540,400 bp Quality-trimmed: 2,573,170 bp (0.1%) Total written (filtered): 2,890,912,320 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10188517 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 30.0% G: 17.7% T: 18.1% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 7457598 7291351.0 0 7457598 2 1687141 1822837.8 0 1687141 3 481240 455709.4 0 481240 4 133910 113927.4 0 133910 5 51263 28481.8 0 51263 6 26682 7120.5 0 26682 7 22140 1780.1 0 22140 8 19590 445.0 0 19590 9 18985 111.3 0 18525 460 10 20366 27.8 1 16766 3600 11 16176 7.0 1 15394 782 12 15211 1.7 1 14558 653 13 13938 0.4 1 13289 649 14 12964 0.4 1 12449 515 15 12532 0.4 1 11953 579 16 11443 0.4 1 10929 514 17 10956 0.4 1 10484 472 18 10395 0.4 1 9895 500 19 9360 0.4 1 8920 440 20 8573 0.4 1 8206 367 21 7733 0.4 1 7415 318 22 7055 0.4 1 6700 355 23 6185 0.4 1 5919 266 24 5855 0.4 1 5621 234 25 5257 0.4 1 5041 216 26 4868 0.4 1 4697 171 27 4803 0.4 1 4577 226 28 4410 0.4 1 4252 158 29 4192 0.4 1 4039 153 30 4125 0.4 1 3949 176 31 3663 0.4 1 3528 135 32 3501 0.4 1 3361 140 33 2934 0.4 1 2809 125 34 2849 0.4 1 2699 150 35 2562 0.4 1 2423 139 36 2446 0.4 1 2320 126 37 2129 0.4 1 2012 117 38 1953 0.4 1 1838 115 39 1857 0.4 1 1754 103 40 1598 0.4 1 1514 84 41 1560 0.4 1 1460 100 42 1301 0.4 1 1216 85 43 1768 0.4 1 1682 86 44 649 0.4 1 598 51 45 867 0.4 1 818 49 46 876 0.4 1 817 59 47 925 0.4 1 856 69 48 956 0.4 1 880 76 49 871 0.4 1 814 57 50 846 0.4 1 791 55 51 791 0.4 1 719 72 52 706 0.4 1 654 52 53 638 0.4 1 582 56 54 506 0.4 1 449 57 55 518 0.4 1 451 67 56 372 0.4 1 322 50 57 372 0.4 1 336 36 58 309 0.4 1 266 43 59 376 0.4 1 322 54 60 328 0.4 1 282 46 61 239 0.4 1 210 29 62 270 0.4 1 234 36 63 251 0.4 1 221 30 64 288 0.4 1 240 48 65 257 0.4 1 221 36 66 284 0.4 1 247 37 67 261 0.4 1 224 37 68 290 0.4 1 254 36 69 357 0.4 1 309 48 70 289 0.4 1 249 40 71 353 0.4 1 303 50 72 385 0.4 1 324 61 73 456 0.4 1 364 92 74 604 0.4 1 416 188 75 3103 0.4 1 536 2567 76 6027 0.4 1 1983 4044 77 6501 0.4 1 2513 3988 78 5433 0.4 1 2049 3384 79 4156 0.4 1 1728 2428 80 2795 0.4 1 1179 1616 81 1950 0.4 1 853 1097 82 1358 0.4 1 626 732 83 922 0.4 1 489 433 84 719 0.4 1 382 337 85 662 0.4 1 395 267 86 571 0.4 1 357 214 87 430 0.4 1 281 149 88 440 0.4 1 332 108 89 393 0.4 1 281 112 90 292 0.4 1 199 93 91 335 0.4 1 225 110 92 232 0.4 1 148 84 93 260 0.4 1 159 101 94 257 0.4 1 168 89 95 330 0.4 1 222 108 96 360 0.4 1 222 138 97 575 0.4 1 351 224 98 474 0.4 1 197 277 99 1064 0.4 1 94 970 100 8321 0.4 1 114 8207 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P07-ATGTCA-READ1-Sequences.txt.gz ============================================= 29165404 sequences processed in total