SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P12-GCCAAT-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-P12-GCCAAT-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 877.68 s (20 us/read; 2.94 M reads/minute). === Summary === Total reads processed: 42,977,789 Reads with adapters: 16,552,644 (38.5%) Reads written (passing filters): 42,977,789 (100.0%) Total basepairs processed: 4,297,778,900 bp Quality-trimmed: 18,939,369 bp (0.4%) Total written (filtered): 4,229,190,784 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16552644 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 24.2% G: 19.0% T: 17.8% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 11686367 10744447.2 0 11686367 2 2876254 2686111.8 0 2876254 3 961686 671528.0 0 961686 4 256006 167882.0 0 256006 5 78181 41970.5 0 78181 6 41464 10492.6 0 41464 7 33753 2623.2 0 33753 8 28433 655.8 0 28433 9 28999 163.9 0 27514 1485 10 27637 41.0 1 24825 2812 11 23734 10.2 1 21786 1948 12 22459 2.6 1 21066 1393 13 19422 0.6 1 18310 1112 14 21171 0.6 1 19974 1197 15 15443 0.6 1 14495 948 16 16630 0.6 1 15615 1015 17 18337 0.6 1 17230 1107 18 11518 0.6 1 10783 735 19 14373 0.6 1 13551 822 20 10370 0.6 1 9689 681 21 10180 0.6 1 9596 584 22 9371 0.6 1 8895 476 23 8573 0.6 1 8136 437 24 7976 0.6 1 7474 502 25 6959 0.6 1 6540 419 26 6618 0.6 1 6212 406 27 6323 0.6 1 5958 365 28 6056 0.6 1 5741 315 29 5406 0.6 1 5105 301 30 5846 0.6 1 5496 350 31 4045 0.6 1 3825 220 32 4472 0.6 1 4198 274 33 3816 0.6 1 3612 204 34 3827 0.6 1 3611 216 35 3225 0.6 1 3043 182 36 3116 0.6 1 2890 226 37 2919 0.6 1 2738 181 38 2563 0.6 1 2425 138 39 2291 0.6 1 2138 153 40 1983 0.6 1 1830 153 41 1813 0.6 1 1638 175 42 1865 0.6 1 1702 163 43 1241 0.6 1 1124 117 44 1325 0.6 1 1159 166 45 1474 0.6 1 1331 143 46 1040 0.6 1 948 92 47 1162 0.6 1 1032 130 48 1197 0.6 1 1074 123 49 1111 0.6 1 984 127 50 972 0.6 1 883 89 51 1045 0.6 1 904 141 52 749 0.6 1 674 75 53 773 0.6 1 690 83 54 663 0.6 1 567 96 55 618 0.6 1 518 100 56 508 0.6 1 400 108 57 435 0.6 1 357 78 58 432 0.6 1 339 93 59 428 0.6 1 341 87 60 413 0.6 1 330 83 61 337 0.6 1 272 65 62 430 0.6 1 324 106 63 346 0.6 1 238 108 64 342 0.6 1 228 114 65 404 0.6 1 226 178 66 812 0.6 1 227 585 67 14488 0.6 1 233 14255 68 26060 0.6 1 806 25254 69 20847 0.6 1 1060 19787 70 14306 0.6 1 938 13368 71 10461 0.6 1 735 9726 72 6057 0.6 1 538 5519 73 3244 0.6 1 346 2898 74 2076 0.6 1 228 1848 75 1345 0.6 1 178 1167 76 878 0.6 1 131 747 77 702 0.6 1 115 587 78 714 0.6 1 116 598 79 568 0.6 1 115 453 80 512 0.6 1 117 395 81 518 0.6 1 110 408 82 471 0.6 1 110 361 83 433 0.6 1 137 296 84 459 0.6 1 115 344 85 360 0.6 1 99 261 86 426 0.6 1 122 304 87 402 0.6 1 101 301 88 472 0.6 1 120 352 89 435 0.6 1 94 341 90 444 0.6 1 56 388 91 610 0.6 1 85 525 92 599 0.6 1 47 552 93 710 0.6 1 30 680 94 1062 0.6 1 30 1032 95 1699 0.6 1 47 1652 96 2597 0.6 1 48 2549 97 4065 0.6 1 95 3970 98 5316 0.6 1 40 5276 99 15263 0.6 1 20 15243 100 94308 0.6 1 78 94230 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P12-GCCAAT-READ2-Sequences.txt.gz ============================================= 42977789 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 42977789 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 321087 (0.75%)