SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_TTAGGC.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_TTAGGC.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 569.15 s (22 us/read; 2.71 M reads/minute). === Summary === Total reads processed: 25,752,634 Reads with adapters: 15,393,563 (59.8%) Reads written (passing filters): 25,752,634 (100.0%) Total basepairs processed: 2,601,016,034 bp Quality-trimmed: 168,252,428 bp (6.5%) Total written (filtered): 2,140,459,636 bp (82.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15393563 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.3% C: 17.2% G: 7.1% T: 19.5% none/other: 20.9% Overview of removed sequences length count expect max.err error counts 1 7645997 6438158.5 0 7645997 2 534336 1609539.6 0 534336 3 291105 402384.9 0 291105 4 245902 100596.2 0 245902 5 222809 25149.1 0 222809 6 221201 6287.3 0 221201 7 227983 1571.8 0 227983 8 176189 393.0 0 176189 9 191707 98.2 0 190234 1473 10 196407 24.6 1 194560 1847 11 135415 6.1 1 133356 2059 12 172560 1.5 1 170422 2138 13 142990 0.4 1 140803 2187 14 139835 0.4 1 137590 2245 15 140839 0.4 1 138493 2346 16 128017 0.4 1 125580 2437 17 141709 0.4 1 138594 3115 18 145963 0.4 1 144065 1898 19 61855 0.4 1 60451 1404 20 97268 0.4 1 95653 1615 21 90319 0.4 1 88627 1692 22 85905 0.4 1 84316 1589 23 72813 0.4 1 71243 1570 24 73060 0.4 1 71571 1489 25 65690 0.4 1 64250 1440 26 57685 0.4 1 55768 1917 27 54892 0.4 1 52716 2176 28 60126 0.4 1 57259 2867 29 41472 0.4 1 39372 2100 30 49205 0.4 1 47594 1611 31 23857 0.4 1 22268 1589 32 37275 0.4 1 33618 3657 33 26224 0.4 1 21303 4921 34 29760 0.4 1 25969 3791 35 22547 0.4 1 20747 1800 36 23176 0.4 1 19483 3693 37 18674 0.4 1 15930 2744 38 16053 0.4 1 13708 2345 39 13968 0.4 1 12793 1175 40 11681 0.4 1 9163 2518 41 10475 0.4 1 8039 2436 42 10739 0.4 1 7353 3386 43 8516 0.4 1 6429 2087 44 7285 0.4 1 5372 1913 45 6868 0.4 1 5558 1310 46 6169 0.4 1 4828 1341 47 4628 0.4 1 3103 1525 48 4038 0.4 1 2397 1641 49 4377 0.4 1 2706 1671 50 4702 0.4 1 2022 2680 51 5287 0.4 1 1938 3349 52 5055 0.4 1 1990 3065 53 3894 0.4 1 1797 2097 54 3728 0.4 1 633 3095 55 3840 0.4 1 948 2892 56 4945 0.4 1 854 4091 57 7122 0.4 1 904 6218 58 7223 0.4 1 746 6477 59 5119 0.4 1 898 4221 60 7815 0.4 1 497 7318 61 10538 0.4 1 562 9976 62 26673 0.4 1 635 26038 63 53981 0.4 1 963 53018 64 17769 0.4 1 917 16852 65 22283 0.4 1 264 22019 66 49178 0.4 1 385 48793 67 173176 0.4 1 558 172618 68 380184 0.4 1 1354 378830 69 1270634 0.4 1 1947 1268687 70 552446 0.4 1 4168 548278 71 201233 0.4 1 913 200320 72 72352 0.4 1 272 72080 73 21277 0.4 1 91 21186 74 11114 0.4 1 52 11062 75 6478 0.4 1 37 6441 76 5114 0.4 1 24 5090 77 6703 0.4 1 33 6670 78 6637 0.4 1 40 6597 79 6056 0.4 1 46 6010 80 5622 0.4 1 26 5596 81 5152 0.4 1 13 5139 82 4865 0.4 1 8 4857 83 4602 0.4 1 14 4588 84 4362 0.4 1 19 4343 85 4613 0.4 1 17 4596 86 4742 0.4 1 29 4713 87 5120 0.4 1 19 5101 88 4899 0.4 1 32 4867 89 4742 0.4 1 24 4718 90 5284 0.4 1 5 5279 91 5575 0.4 1 11 5564 92 5872 0.4 1 12 5860 93 6133 0.4 1 4 6129 94 6580 0.4 1 8 6572 95 7236 0.4 1 6 7230 96 8258 0.4 1 3 8255 97 9049 0.4 1 5 9044 98 10113 0.4 1 1 10112 99 11510 0.4 1 0 11510 100 22958 0.4 1 2 22956 101 96156 0.4 1 5 96151 RUN STATISTICS FOR INPUT FILE: 2112_lane1_TTAGGC.fastq.gz ============================================= 25752634 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3234303 (12.6%)