SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_9_s1_R1_val_1.fq.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; default (inconclusive auto-detection)) 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 2 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 ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_9_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 568.18 s (18 us/read; 3.39 M reads/minute). === Summary === Total reads processed: 32,090,732 Reads with adapters: 16,247,494 (50.6%) Reads written (passing filters): 32,090,732 (100.0%) Total basepairs processed: 2,422,296,960 bp Quality-trimmed: 5,121,841 bp (0.2%) Total written (filtered): 2,397,514,901 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16247494 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.6% C: 11.2% G: 11.0% T: 37.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13951064 8022683.0 0 13951064 2 1714451 2005670.8 0 1714451 3 463830 501417.7 0 463830 4 67603 125354.4 0 67603 5 6836 31338.6 0 6836 6 7175 7834.7 0 7175 7 2246 1958.7 0 2246 8 1054 489.7 0 1054 9 1330 122.4 0 441 889 10 1773 30.6 1 343 1430 11 2274 7.7 1 300 1974 12 1304 1.9 1 261 1043 13 1582 0.5 1 0 1582 14 2362 0.5 1 0 2362 15 4762 0.5 1 0 4762 16 8728 0.5 1 0 8728 17 7514 0.5 1 0 7514 18 361 0.5 1 0 361 19 60 0.5 1 0 60 20 28 0.5 1 0 28 21 36 0.5 1 0 36 22 32 0.5 1 0 32 23 27 0.5 1 0 27 24 22 0.5 1 0 22 25 42 0.5 1 0 42 26 42 0.5 1 0 42 27 40 0.5 1 0 40 28 35 0.5 1 0 35 29 35 0.5 1 0 35 30 34 0.5 1 0 34 31 46 0.5 1 0 46 32 30 0.5 1 0 30 33 33 0.5 1 0 33 34 18 0.5 1 0 18 35 31 0.5 1 0 31 36 26 0.5 1 0 26 37 42 0.5 1 0 42 38 22 0.5 1 0 22 39 25 0.5 1 0 25 40 33 0.5 1 0 33 41 25 0.5 1 0 25 42 21 0.5 1 0 21 43 36 0.5 1 0 36 44 23 0.5 1 0 23 45 30 0.5 1 0 30 46 27 0.5 1 0 27 47 25 0.5 1 0 25 48 25 0.5 1 0 25 49 26 0.5 1 0 26 50 20 0.5 1 0 20 51 16 0.5 1 0 16 52 23 0.5 1 0 23 53 18 0.5 1 0 18 54 9 0.5 1 0 9 55 14 0.5 1 0 14 56 13 0.5 1 0 13 57 15 0.5 1 0 15 58 15 0.5 1 0 15 59 16 0.5 1 0 16 60 11 0.5 1 0 11 61 16 0.5 1 0 16 62 11 0.5 1 0 11 63 16 0.5 1 0 16 64 12 0.5 1 0 12 65 11 0.5 1 0 11 66 8 0.5 1 0 8 67 6 0.5 1 0 6 68 6 0.5 1 0 6 69 3 0.5 1 0 3 70 5 0.5 1 0 5 71 2 0.5 1 0 2 72 2 0.5 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_9_s1_R1_val_1.fq.gz ============================================= 32090732 sequences processed in total