SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_6_s1_R2_val_2.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_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 395.47 s (16 us/read; 3.65 M reads/minute). === Summary === Total reads processed: 24,080,119 Reads with adapters: 8,546,733 (35.5%) Reads written (passing filters): 24,080,119 (100.0%) Total basepairs processed: 1,782,249,619 bp Quality-trimmed: 1,044,332 bp (0.1%) Total written (filtered): 1,771,289,577 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8546733 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 14.7% G: 3.9% T: 35.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7935438 6020029.8 0 7935438 2 414461 1505007.4 0 414461 3 127936 376251.9 0 127936 4 20586 94063.0 0 20586 5 2037 23515.7 0 2037 6 2157 5878.9 0 2157 7 484 1469.7 0 484 8 249 367.4 0 249 9 1575 91.9 0 1326 249 10 1311 23.0 1 166 1145 11 1791 5.7 1 614 1177 12 1769 1.4 1 251 1518 13 3146 0.4 1 0 3146 14 5998 0.4 1 0 5998 15 8811 0.4 1 0 8811 16 10983 0.4 1 0 10983 17 6124 0.4 1 0 6124 18 598 0.4 1 0 598 19 104 0.4 1 0 104 20 55 0.4 1 0 55 21 50 0.4 1 0 50 22 64 0.4 1 0 64 23 63 0.4 1 0 63 24 55 0.4 1 0 55 25 68 0.4 1 0 68 26 62 0.4 1 0 62 27 53 0.4 1 0 53 28 49 0.4 1 0 49 29 55 0.4 1 0 55 30 55 0.4 1 0 55 31 60 0.4 1 0 60 32 33 0.4 1 0 33 33 37 0.4 1 0 37 34 30 0.4 1 0 30 35 23 0.4 1 0 23 36 21 0.4 1 0 21 37 13 0.4 1 0 13 38 21 0.4 1 0 21 39 25 0.4 1 0 25 40 15 0.4 1 0 15 41 16 0.4 1 0 16 42 27 0.4 1 0 27 43 14 0.4 1 0 14 44 15 0.4 1 0 15 45 21 0.4 1 0 21 46 15 0.4 1 0 15 47 12 0.4 1 0 12 48 5 0.4 1 0 5 49 19 0.4 1 0 19 50 7 0.4 1 0 7 51 7 0.4 1 0 7 52 15 0.4 1 0 15 53 8 0.4 1 0 8 54 8 0.4 1 0 8 55 5 0.4 1 0 5 56 6 0.4 1 0 6 57 6 0.4 1 0 6 58 9 0.4 1 0 9 59 9 0.4 1 0 9 60 4 0.4 1 0 4 61 2 0.4 1 0 2 62 5 0.4 1 0 5 63 10 0.4 1 0 10 64 4 0.4 1 0 4 65 6 0.4 1 0 6 66 4 0.4 1 0 4 67 2 0.4 1 0 2 68 2 0.4 1 0 2 69 1 0.4 1 0 1 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_R2_val_2.fq.gz ============================================= 24080119 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24080119 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 116633 (0.48%)