SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_8_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_8_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 511.70 s (17 us/read; 3.49 M reads/minute). === Summary === Total reads processed: 29,761,837 Reads with adapters: 6,230,529 (20.9%) Reads written (passing filters): 29,761,837 (100.0%) Total basepairs processed: 2,705,142,381 bp Quality-trimmed: 9,093,824 bp (0.3%) Total written (filtered): 2,687,730,288 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6230529 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.5% C: 13.9% G: 32.7% T: 30.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4708845 7440459.2 0 4708845 2 1035200 1860114.8 0 1035200 3 454845 465028.7 0 454845 4 15837 116257.2 0 15837 5 10378 29064.3 0 10378 6 3993 7266.1 0 3993 7 162 1816.5 0 162 8 166 454.1 0 166 9 234 113.5 0 36 198 10 238 28.4 1 2 236 11 62 7.1 1 0 62 12 8 1.8 1 0 8 13 1 1.8 1 0 1 14 2 1.8 1 0 2 15 9 1.8 1 0 9 16 5 1.8 1 0 5 17 3 1.8 1 0 3 18 7 1.8 1 0 7 19 11 1.8 1 0 11 20 5 1.8 1 0 5 21 2 1.8 1 0 2 22 14 1.8 1 0 14 23 11 1.8 1 0 11 24 5 1.8 1 0 5 25 11 1.8 1 0 11 26 7 1.8 1 0 7 27 14 1.8 1 0 14 28 12 1.8 1 0 12 29 12 1.8 1 0 12 30 11 1.8 1 0 11 31 6 1.8 1 0 6 32 2 1.8 1 0 2 33 6 1.8 1 0 6 34 15 1.8 1 0 15 35 12 1.8 1 0 12 36 12 1.8 1 0 12 37 10 1.8 1 0 10 38 11 1.8 1 0 11 39 4 1.8 1 0 4 40 11 1.8 1 0 11 41 6 1.8 1 0 6 42 2 1.8 1 0 2 43 4 1.8 1 0 4 44 10 1.8 1 1 9 45 15 1.8 1 0 15 46 13 1.8 1 0 13 47 12 1.8 1 0 12 48 6 1.8 1 0 6 49 8 1.8 1 0 8 50 8 1.8 1 0 8 51 15 1.8 1 0 15 52 7 1.8 1 0 7 53 13 1.8 1 0 13 54 7 1.8 1 0 7 55 7 1.8 1 0 7 56 4 1.8 1 0 4 57 10 1.8 1 0 10 58 4 1.8 1 0 4 59 7 1.8 1 0 7 60 8 1.8 1 0 8 61 3 1.8 1 0 3 62 6 1.8 1 0 6 63 3 1.8 1 0 3 64 7 1.8 1 0 7 65 7 1.8 1 0 7 66 7 1.8 1 0 7 67 5 1.8 1 0 5 68 1 1.8 1 0 1 69 2 1.8 1 0 2 70 7 1.8 1 0 7 71 5 1.8 1 0 5 72 5 1.8 1 0 5 73 5 1.8 1 0 5 74 5 1.8 1 0 5 75 4 1.8 1 0 4 76 9 1.8 1 0 9 77 7 1.8 1 0 7 78 7 1.8 1 0 7 79 3 1.8 1 0 3 80 5 1.8 1 0 5 81 6 1.8 1 0 6 82 3 1.8 1 0 3 83 4 1.8 1 0 4 84 6 1.8 1 0 6 85 4 1.8 1 0 4 86 3 1.8 1 0 3 87 1 1.8 1 0 1 88 4 1.8 1 0 4 89 3 1.8 1 0 3 90 3 1.8 1 0 3 91 3 1.8 1 0 3 92 5 1.8 1 0 5 93 4 1.8 1 0 4 94 1 1.8 1 0 1 95 3 1.8 1 0 3 96 2 1.8 1 0 2 97 3 1.8 1 0 3 98 2 1.8 1 0 2 99 1 1.8 1 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_8_s1_R2.fastq.gz ============================================= 29761837 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29761837 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 142299 (0.48%)