SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_6_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_6_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 425.86 s (18 us/read; 3.39 M reads/minute). === Summary === Total reads processed: 24,080,119 Reads with adapters: 11,885,324 (49.4%) Reads written (passing filters): 24,080,119 (100.0%) Total basepairs processed: 1,778,574,588 bp Quality-trimmed: 1,878,979 bp (0.1%) Total written (filtered): 1,761,896,293 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11885324 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 12.0% G: 11.9% T: 36.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9952709 6020029.8 0 9952709 2 1470198 1505007.4 0 1470198 3 366956 376251.9 0 366956 4 48963 94063.0 0 48963 5 4202 23515.7 0 4202 6 4623 5878.9 0 4623 7 2246 1469.7 0 2246 8 1172 367.4 0 1172 9 981 91.9 0 286 695 10 1850 23.0 1 561 1289 11 1284 5.7 1 245 1039 12 1260 1.4 1 285 975 13 1829 0.4 1 0 1829 14 2752 0.4 1 0 2752 15 5214 0.4 1 0 5214 16 9578 0.4 1 0 9578 17 7522 0.4 1 0 7522 18 536 0.4 1 0 536 19 118 0.4 1 0 118 20 59 0.4 1 0 59 21 50 0.4 1 0 50 22 53 0.4 1 0 53 23 46 0.4 1 0 46 24 83 0.4 1 0 83 25 68 0.4 1 0 68 26 62 0.4 1 0 62 27 51 0.4 1 0 51 28 48 0.4 1 0 48 29 59 0.4 1 0 59 30 39 0.4 1 0 39 31 60 0.4 1 0 60 32 54 0.4 1 0 54 33 45 0.4 1 0 45 34 27 0.4 1 0 27 35 30 0.4 1 0 30 36 29 0.4 1 0 29 37 30 0.4 1 0 30 38 19 0.4 1 0 19 39 30 0.4 1 0 30 40 33 0.4 1 0 33 41 24 0.4 1 0 24 42 35 0.4 1 0 35 43 25 0.4 1 0 25 44 27 0.4 1 0 27 45 26 0.4 1 0 26 46 21 0.4 1 0 21 47 12 0.4 1 0 12 48 18 0.4 1 0 18 49 10 0.4 1 0 10 50 16 0.4 1 0 16 51 16 0.4 1 0 16 52 13 0.4 1 0 13 53 8 0.4 1 0 8 54 11 0.4 1 0 11 55 14 0.4 1 0 14 56 10 0.4 1 0 10 57 7 0.4 1 0 7 58 4 0.4 1 0 4 59 10 0.4 1 0 10 60 10 0.4 1 0 10 61 7 0.4 1 0 7 62 3 0.4 1 0 3 63 4 0.4 1 0 4 64 6 0.4 1 0 6 65 2 0.4 1 0 2 66 1 0.4 1 0 1 67 3 0.4 1 0 3 68 6 0.4 1 0 6 69 3 0.4 1 0 3 70 1 0.4 1 0 1 71 1 0.4 1 0 1 72 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_6_s1_R1_val_1.fq.gz ============================================= 24080119 sequences processed in total