SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_GCCAAT.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_GCCAAT.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 546.65 s (22 us/read; 2.72 M reads/minute). === Summary === Total reads processed: 24,792,684 Reads with adapters: 13,652,723 (55.1%) Reads written (passing filters): 24,792,684 (100.0%) Total basepairs processed: 2,504,061,084 bp Quality-trimmed: 162,739,913 bp (6.5%) Total written (filtered): 2,103,508,344 bp (84.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13652723 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.8% C: 17.3% G: 6.2% T: 17.8% none/other: 21.1% Overview of removed sequences length count expect max.err error counts 1 8285474 6198171.0 0 8285474 2 559416 1549542.8 0 559416 3 216338 387385.7 0 216338 4 143815 96846.4 0 143815 5 117955 24211.6 0 117955 6 111642 6052.9 0 111642 7 108539 1513.2 0 108539 8 86050 378.3 0 86050 9 91517 94.6 0 90714 803 10 88443 23.6 1 87249 1194 11 62625 5.9 1 61504 1121 12 74455 1.5 1 73328 1127 13 63753 0.4 1 62538 1215 14 59311 0.4 1 58269 1042 15 59539 0.4 1 58231 1308 16 55250 0.4 1 54149 1101 17 58732 0.4 1 57225 1507 18 58521 0.4 1 57593 928 19 27839 0.4 1 27131 708 20 40399 0.4 1 39530 869 21 37610 0.4 1 36794 816 22 34021 0.4 1 33233 788 23 30471 0.4 1 29631 840 24 29774 0.4 1 28829 945 25 28103 0.4 1 27162 941 26 24228 0.4 1 22988 1240 27 23744 0.4 1 22120 1624 28 25066 0.4 1 22672 2394 29 19955 0.4 1 18259 1696 30 20569 0.4 1 19245 1324 31 12893 0.4 1 11639 1254 32 17686 0.4 1 14475 3211 33 16816 0.4 1 10050 6766 34 13947 0.4 1 12215 1732 35 10733 0.4 1 8237 2496 36 10850 0.4 1 8775 2075 37 10956 0.4 1 8744 2212 38 8624 0.4 1 6206 2418 39 7255 0.4 1 5843 1412 40 7962 0.4 1 5111 2851 41 8308 0.4 1 4244 4064 42 8798 0.4 1 4247 4551 43 6029 0.4 1 3510 2519 44 6198 0.4 1 3128 3070 45 5386 0.4 1 3247 2139 46 4678 0.4 1 2600 2078 47 3677 0.4 1 1794 1883 48 3427 0.4 1 1496 1931 49 3113 0.4 1 1630 1483 50 3613 0.4 1 1203 2410 51 5273 0.4 1 1201 4072 52 4675 0.4 1 1313 3362 53 3187 0.4 1 1168 2019 54 3635 0.4 1 364 3271 55 3449 0.4 1 596 2853 56 5070 0.4 1 589 4481 57 7323 0.4 1 647 6676 58 8103 0.4 1 525 7578 59 4762 0.4 1 627 4135 60 7877 0.4 1 311 7566 61 10083 0.4 1 362 9721 62 26621 0.4 1 392 26229 63 44918 0.4 1 850 44068 64 14573 0.4 1 727 13846 65 18391 0.4 1 213 18178 66 41246 0.4 1 289 40957 67 143024 0.4 1 520 142504 68 320571 0.4 1 1156 319415 69 1097289 0.4 1 1900 1095389 70 537660 0.4 1 4063 533597 71 189910 0.4 1 942 188968 72 67056 0.4 1 296 66760 73 18900 0.4 1 81 18819 74 10062 0.4 1 58 10004 75 5888 0.4 1 47 5841 76 4721 0.4 1 38 4683 77 5866 0.4 1 38 5828 78 5884 0.4 1 60 5824 79 5522 0.4 1 47 5475 80 4957 0.4 1 19 4938 81 4479 0.4 1 12 4467 82 4324 0.4 1 9 4315 83 4003 0.4 1 12 3991 84 3995 0.4 1 13 3982 85 3853 0.4 1 12 3841 86 4026 0.4 1 16 4010 87 4437 0.4 1 22 4415 88 4100 0.4 1 15 4085 89 4291 0.4 1 20 4271 90 4505 0.4 1 5 4500 91 4791 0.4 1 9 4782 92 5060 0.4 1 16 5044 93 5354 0.4 1 4 5350 94 5880 0.4 1 6 5874 95 6341 0.4 1 5 6336 96 7141 0.4 1 4 7137 97 8080 0.4 1 1 8079 98 8935 0.4 1 1 8934 99 10431 0.4 1 2 10429 100 20510 0.4 1 3 20507 101 87588 0.4 1 7 87581 RUN STATISTICS FOR INPUT FILE: 2112_lane1_GCCAAT.fastq.gz ============================================= 24792684 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2906782 (11.7%)