SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_TGACCA.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 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 before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_TGACCA.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 222.28 s (24 us/read; 2.48 M reads/minute). === Summary === Total reads processed: 9,188,940 Reads with adapters: 7,714,396 (84.0%) Reads written (passing filters): 9,188,940 (100.0%) Total basepairs processed: 928,082,940 bp Quality-trimmed: 208,253,890 bp (22.4%) Total written (filtered): 346,199,587 bp (37.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7714396 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.0% C: 5.5% G: 4.6% T: 5.6% none/other: 64.4% Overview of removed sequences length count expect max.err error counts 1 1492673 2297235.0 0 1492673 2 128598 574308.8 0 128598 3 46570 143577.2 0 46570 4 41159 35894.3 0 41159 5 37536 8973.6 0 37536 6 41569 2243.4 0 41569 7 48187 560.8 0 48187 8 28646 140.2 0 28646 9 34011 35.1 0 33552 459 10 40836 8.8 1 40446 390 11 21070 2.2 1 20614 456 12 39375 0.5 1 38852 523 13 28223 0.1 1 27712 511 14 30477 0.1 1 30009 468 15 31572 0.1 1 30949 623 16 34270 0.1 1 33591 679 17 32392 0.1 1 31586 806 18 37144 0.1 1 36578 566 19 16557 0.1 1 16121 436 20 27628 0.1 1 27119 509 21 27318 0.1 1 26715 603 22 29792 0.1 1 29190 602 23 20283 0.1 1 19662 621 24 23742 0.1 1 23010 732 25 27134 0.1 1 26401 733 26 21110 0.1 1 19750 1360 27 24652 0.1 1 22661 1991 28 29900 0.1 1 27077 2823 29 20898 0.1 1 18877 2021 30 26378 0.1 1 24966 1412 31 11675 0.1 1 10195 1480 32 24841 0.1 1 20740 4101 33 19835 0.1 1 13337 6498 34 22072 0.1 1 17701 4371 35 17506 0.1 1 15765 1741 36 19797 0.1 1 15998 3799 37 16923 0.1 1 12762 4161 38 14306 0.1 1 12662 1644 39 26208 0.1 1 13199 13009 40 19199 0.1 1 10916 8283 41 20520 0.1 1 10636 9884 42 18073 0.1 1 9522 8551 43 14909 0.1 1 9560 5349 44 16890 0.1 1 8049 8841 45 15620 0.1 1 10542 5078 46 12395 0.1 1 8215 4180 47 10591 0.1 1 5173 5418 48 9609 0.1 1 4173 5436 49 9523 0.1 1 5244 4279 50 9295 0.1 1 3891 5404 51 13901 0.1 1 3851 10050 52 13243 0.1 1 5125 8118 53 8982 0.1 1 4127 4855 54 9199 0.1 1 1093 8106 55 8068 0.1 1 1833 6235 56 12312 0.1 1 1891 10421 57 16344 0.1 1 2128 14216 58 16997 0.1 1 1515 15482 59 9772 0.1 1 1717 8055 60 15043 0.1 1 825 14218 61 18869 0.1 1 914 17955 62 60104 0.1 1 885 59219 63 81495 0.1 1 1695 79800 64 21625 0.1 1 1087 20538 65 27271 0.1 1 267 27004 66 62437 0.1 1 500 61937 67 216127 0.1 1 644 215483 68 512969 0.1 1 1417 511552 69 1759541 0.1 1 2378 1757163 70 1031227 0.1 1 5431 1025796 71 385531 0.1 1 1504 384027 72 136018 0.1 1 455 135563 73 37324 0.1 1 158 37166 74 18788 0.1 1 90 18698 75 10612 0.1 1 56 10556 76 8749 0.1 1 51 8698 77 11805 0.1 1 34 11771 78 11502 0.1 1 51 11451 79 10571 0.1 1 56 10515 80 9179 0.1 1 14 9165 81 7981 0.1 1 17 7964 82 7509 0.1 1 12 7497 83 6703 0.1 1 18 6685 84 6606 0.1 1 19 6587 85 6518 0.1 1 27 6491 86 6887 0.1 1 43 6844 87 7238 0.1 1 38 7200 88 6963 0.1 1 48 6915 89 7086 0.1 1 61 7025 90 7376 0.1 1 7 7369 91 7796 0.1 1 10 7786 92 8320 0.1 1 10 8310 93 8758 0.1 1 3 8755 94 9533 0.1 1 11 9522 95 10141 0.1 1 3 10138 96 11512 0.1 1 3 11509 97 13094 0.1 1 5 13089 98 14343 0.1 1 3 14340 99 16413 0.1 1 1 16412 100 32725 0.1 1 10 32715 101 135802 0.1 1 12 135790 RUN STATISTICS FOR INPUT FILE: 2112_lane1_TGACCA.fastq.gz ============================================= 9188940 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 4981933 (54.2%)