SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_2_s1_R2.fastq.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: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 bp All Read 1 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 GATCGTCGGACT /mnt/owl/nightingales/C_virginica/zr2096_2_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 523.49 s (17 us/read; 3.53 M reads/minute). === Summary === Total reads processed: 30,798,582 Reads with adapters: 7,597,858 (24.7%) Reads written (passing filters): 30,798,582 (100.0%) Total basepairs processed: 2,666,689,257 bp Quality-trimmed: 9,450,051 bp (0.4%) Total written (filtered): 2,647,320,826 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 7597858 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 21.7% C: 14.3% G: 35.6% T: 28.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5888183 7699645.5 0 5888183 2 1196023 1924911.4 0 1196023 3 476916 481227.8 0 476916 4 16920 120307.0 0 16920 5 12402 30076.7 0 12402 6 5297 7519.2 0 5297 7 477 1879.8 0 477 8 240 469.9 0 240 9 279 117.5 0 37 242 10 309 29.4 1 6 303 11 96 7.3 1 0 96 12 8 1.8 1 0 8 13 6 1.8 1 0 6 14 8 1.8 1 0 8 15 7 1.8 1 0 7 16 8 1.8 1 0 8 17 5 1.8 1 0 5 18 9 1.8 1 0 9 19 13 1.8 1 0 13 20 9 1.8 1 0 9 21 10 1.8 1 0 10 22 9 1.8 1 0 9 23 18 1.8 1 0 18 24 5 1.8 1 1 4 25 14 1.8 1 0 14 26 8 1.8 1 0 8 27 47 1.8 1 0 47 28 15 1.8 1 0 15 29 9 1.8 1 0 9 30 5 1.8 1 0 5 31 7 1.8 1 0 7 32 9 1.8 1 0 9 33 12 1.8 1 0 12 34 8 1.8 1 0 8 35 8 1.8 1 0 8 36 10 1.8 1 0 10 37 10 1.8 1 0 10 38 5 1.8 1 0 5 39 12 1.8 1 0 12 40 8 1.8 1 0 8 41 5 1.8 1 0 5 42 9 1.8 1 0 9 43 7 1.8 1 0 7 44 11 1.8 1 0 11 45 10 1.8 1 0 10 46 18 1.8 1 0 18 47 14 1.8 1 0 14 48 10 1.8 1 0 10 49 6 1.8 1 0 6 50 17 1.8 1 0 17 51 10 1.8 1 0 10 52 12 1.8 1 0 12 53 18 1.8 1 0 18 54 11 1.8 1 0 11 55 12 1.8 1 0 12 56 10 1.8 1 0 10 57 2 1.8 1 0 2 58 3 1.8 1 0 3 59 10 1.8 1 0 10 60 4 1.8 1 0 4 61 10 1.8 1 0 10 62 11 1.8 1 0 11 63 13 1.8 1 0 13 64 10 1.8 1 0 10 65 12 1.8 1 0 12 66 9 1.8 1 0 9 67 10 1.8 1 0 10 68 5 1.8 1 0 5 69 2 1.8 1 0 2 70 9 1.8 1 0 9 71 5 1.8 1 0 5 72 7 1.8 1 0 7 73 5 1.8 1 0 5 74 14 1.8 1 0 14 75 6 1.8 1 0 6 76 6 1.8 1 0 6 77 3 1.8 1 0 3 78 3 1.8 1 0 3 79 8 1.8 1 0 8 80 4 1.8 1 0 4 81 5 1.8 1 0 5 82 4 1.8 1 0 4 83 4 1.8 1 0 4 84 3 1.8 1 0 3 85 5 1.8 1 0 5 86 2 1.8 1 0 2 87 3 1.8 1 0 3 88 4 1.8 1 0 4 89 4 1.8 1 0 4 90 1 1.8 1 0 1 91 5 1.8 1 0 5 92 2 1.8 1 0 2 93 2 1.8 1 0 2 94 4 1.8 1 0 4 95 4 1.8 1 0 4 96 3 1.8 1 1 2 97 3 1.8 1 0 3 98 3 1.8 1 0 3 100 2 1.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_2_s1_R2.fastq.gz ============================================= 30798582 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 30798582 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 221380 (0.72%)