SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P01-AGTTCC-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/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-P01-AGTTCC-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 523.04 s (21 us/read; 2.89 M reads/minute). === Summary === Total reads processed: 25,210,785 Reads with adapters: 9,888,434 (39.2%) Reads written (passing filters): 25,210,785 (100.0%) Total basepairs processed: 2,521,078,500 bp Quality-trimmed: 18,588,718 bp (0.7%) Total written (filtered): 2,463,345,403 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9888434 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.4% C: 23.2% G: 18.3% T: 17.5% none/other: 2.6% Overview of removed sequences length count expect max.err error counts 1 6948743 6302696.2 0 6948743 2 1704518 1575674.1 0 1704518 3 572971 393918.5 0 572971 4 142831 98479.6 0 142831 5 43560 24619.9 0 43560 6 19916 6155.0 0 19916 7 15727 1538.7 0 15727 8 13555 384.7 0 13555 9 13490 96.2 0 12720 770 10 13548 24.0 1 11534 2014 11 11312 6.0 1 9992 1320 12 10372 1.5 1 9386 986 13 9299 0.4 1 8465 834 14 10071 0.4 1 9143 928 15 6989 0.4 1 6384 605 16 7644 0.4 1 6950 694 17 9080 0.4 1 8268 812 18 5315 0.4 1 4828 487 19 6906 0.4 1 6246 660 20 4602 0.4 1 4178 424 21 4705 0.4 1 4270 435 22 4067 0.4 1 3605 462 23 3843 0.4 1 3411 432 24 3689 0.4 1 3213 476 25 3045 0.4 1 2712 333 26 2851 0.4 1 2531 320 27 2752 0.4 1 2408 344 28 2747 0.4 1 2397 350 29 2401 0.4 1 2108 293 30 2834 0.4 1 2496 338 31 1702 0.4 1 1485 217 32 1966 0.4 1 1709 257 33 1647 0.4 1 1418 229 34 1551 0.4 1 1312 239 35 1420 0.4 1 1203 217 36 1507 0.4 1 1280 227 37 1218 0.4 1 1025 193 38 1253 0.4 1 1015 238 39 1008 0.4 1 859 149 40 900 0.4 1 767 133 41 879 0.4 1 692 187 42 924 0.4 1 743 181 43 651 0.4 1 518 133 44 650 0.4 1 503 147 45 856 0.4 1 687 169 46 517 0.4 1 384 133 47 593 0.4 1 442 151 48 692 0.4 1 544 148 49 568 0.4 1 405 163 50 539 0.4 1 417 122 51 721 0.4 1 544 177 52 450 0.4 1 312 138 53 403 0.4 1 306 97 54 383 0.4 1 288 95 55 354 0.4 1 285 69 56 318 0.4 1 238 80 57 290 0.4 1 206 84 58 266 0.4 1 171 95 59 299 0.4 1 217 82 60 265 0.4 1 197 68 61 324 0.4 1 215 109 62 298 0.4 1 170 128 63 300 0.4 1 200 100 64 290 0.4 1 182 108 65 294 0.4 1 169 125 66 490 0.4 1 137 353 67 15661 0.4 1 185 15476 68 18904 0.4 1 681 18223 69 18753 0.4 1 531 18222 70 19407 0.4 1 575 18832 71 10805 0.4 1 566 10239 72 7808 0.4 1 380 7428 73 5518 0.4 1 286 5232 74 3060 0.4 1 220 2840 75 1716 0.4 1 158 1558 76 1222 0.4 1 118 1104 77 1090 0.4 1 150 940 78 760 0.4 1 93 667 79 589 0.4 1 99 490 80 635 0.4 1 88 547 81 453 0.4 1 97 356 82 444 0.4 1 78 366 83 425 0.4 1 82 343 84 384 0.4 1 74 310 85 337 0.4 1 50 287 86 325 0.4 1 53 272 87 371 0.4 1 68 303 88 375 0.4 1 58 317 89 381 0.4 1 43 338 90 448 0.4 1 55 393 91 568 0.4 1 64 504 92 552 0.4 1 27 525 93 608 0.4 1 16 592 94 805 0.4 1 21 784 95 1276 0.4 1 53 1223 96 2029 0.4 1 45 1984 97 3603 0.4 1 101 3502 98 5212 0.4 1 37 5175 99 15023 0.4 1 18 15005 100 118718 0.4 1 54 118664 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz ============================================= 25210785 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 25210785 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 363867 (1.44%)