SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_ACAGTG.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_ACAGTG.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 397.25 s (23 us/read; 2.62 M reads/minute). === Summary === Total reads processed: 17,327,210 Reads with adapters: 10,263,059 (59.2%) Reads written (passing filters): 17,327,210 (100.0%) Total basepairs processed: 1,750,048,210 bp Quality-trimmed: 185,921,084 bp (10.6%) Total written (filtered): 1,261,527,856 bp (72.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10263059 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.4% C: 14.1% G: 6.2% T: 13.4% none/other: 38.0% Overview of removed sequences length count expect max.err error counts 1 4187128 4331802.5 0 4187128 2 454105 1082950.6 0 454105 3 173887 270737.7 0 173887 4 132573 67684.4 0 132573 5 112014 16921.1 0 112014 6 112058 4230.3 0 112058 7 118966 1057.6 0 118966 8 75644 264.4 0 75644 9 82132 66.1 0 81258 874 10 91566 16.5 1 90662 904 11 49449 4.1 1 48579 870 12 74402 1.0 1 73557 845 13 54356 0.3 1 53474 882 14 54152 0.3 1 53335 817 15 51633 0.3 1 50745 888 16 45761 0.3 1 44877 884 17 50139 0.3 1 48938 1201 18 49514 0.3 1 48856 658 19 20534 0.3 1 20080 454 20 33290 0.3 1 32710 580 21 29372 0.3 1 28697 675 22 33080 0.3 1 32419 661 23 19223 0.3 1 18693 530 24 21075 0.3 1 20530 545 25 21912 0.3 1 21297 615 26 18258 0.3 1 16907 1351 27 19242 0.3 1 17472 1770 28 22623 0.3 1 19941 2682 29 13645 0.3 1 12102 1543 30 17134 0.3 1 15866 1268 31 8771 0.3 1 7489 1282 32 15705 0.3 1 11988 3717 33 11427 0.3 1 7518 3909 34 11995 0.3 1 9523 2472 35 8576 0.3 1 6341 2235 36 14389 0.3 1 7992 6397 37 11073 0.3 1 7217 3856 38 10008 0.3 1 8264 1744 39 4031 0.3 1 2275 1756 40 8813 0.3 1 5164 3649 41 7361 0.3 1 2676 4685 42 8430 0.3 1 3157 5273 43 5950 0.3 1 3071 2879 44 4902 0.3 1 2756 2146 45 4218 0.3 1 2813 1405 46 4226 0.3 1 2704 1522 47 3516 0.3 1 1742 1774 48 3322 0.3 1 1428 1894 49 3799 0.3 1 1840 1959 50 4609 0.3 1 1432 3177 51 5145 0.3 1 1432 3713 52 5288 0.3 1 1634 3654 53 3974 0.3 1 1619 2355 54 4262 0.3 1 522 3740 55 4224 0.3 1 812 3412 56 5448 0.3 1 816 4632 57 8442 0.3 1 1008 7434 58 8455 0.3 1 857 7598 59 5746 0.3 1 910 4836 60 9462 0.3 1 529 8933 61 12883 0.3 1 591 12292 62 34190 0.3 1 673 33517 63 60413 0.3 1 1245 59168 64 20284 0.3 1 1108 19176 65 25390 0.3 1 305 25085 66 57515 0.3 1 449 57066 67 203411 0.3 1 694 202717 68 453643 0.3 1 1657 451986 69 1544843 0.3 1 2603 1542240 70 698942 0.3 1 5353 693589 71 251952 0.3 1 1270 250682 72 90056 0.3 1 392 89664 73 25840 0.3 1 109 25731 74 13657 0.3 1 61 13596 75 7878 0.3 1 44 7834 76 6202 0.3 1 49 6153 77 8053 0.3 1 48 8005 78 8207 0.3 1 47 8160 79 7538 0.3 1 57 7481 80 6582 0.3 1 19 6563 81 5978 0.3 1 16 5962 82 5811 0.3 1 12 5799 83 5628 0.3 1 13 5615 84 5305 0.3 1 15 5290 85 5343 0.3 1 17 5326 86 5444 0.3 1 29 5415 87 5906 0.3 1 18 5888 88 5690 0.3 1 25 5665 89 5649 0.3 1 40 5609 90 6103 0.3 1 16 6087 91 6211 0.3 1 2 6209 92 6664 0.3 1 13 6651 93 6982 0.3 1 4 6978 94 7732 0.3 1 11 7721 95 7979 0.3 1 4 7975 96 9450 0.3 1 2 9448 97 10273 0.3 1 1 10272 98 11315 0.3 1 2 11313 99 13205 0.3 1 1 13204 100 26252 0.3 1 2 26250 101 108226 0.3 1 4 108222 RUN STATISTICS FOR INPUT FILE: 2112_lane1_ACAGTG.fastq.gz ============================================= 17327210 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3919105 (22.6%)