SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_4_s1_R1.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 TGGAATTCTCGG /mnt/owl/nightingales/C_virginica/zr2096_4_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 434.29 s (18 us/read; 3.36 M reads/minute). === Summary === Total reads processed: 24,341,968 Reads with adapters: 10,689,983 (43.9%) Reads written (passing filters): 24,341,968 (100.0%) Total basepairs processed: 2,140,220,885 bp Quality-trimmed: 6,722,337 bp (0.3%) Total written (filtered): 2,120,093,942 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 10689983 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.7% G: 23.7% T: 43.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8852591 6085492.0 0 8852591 2 1242097 1521373.0 0 1242097 3 476517 380343.2 0 476517 4 75989 95085.8 0 75989 5 29444 23771.5 0 29444 6 7498 5942.9 0 7498 7 3157 1485.7 0 3157 8 64 371.4 0 64 9 52 92.9 0 11 41 10 119 23.2 1 1 118 11 84 5.8 1 0 84 12 35 1.5 1 0 35 13 40 1.5 1 0 40 14 48 1.5 1 0 48 15 30 1.5 1 0 30 16 29 1.5 1 0 29 17 27 1.5 1 1 26 18 37 1.5 1 0 37 19 18 1.5 1 0 18 20 22 1.5 1 0 22 21 26 1.5 1 0 26 22 43 1.5 1 0 43 23 35 1.5 1 0 35 24 31 1.5 1 0 31 25 29 1.5 1 0 29 26 38 1.5 1 0 38 27 31 1.5 1 0 31 28 42 1.5 1 0 42 29 32 1.5 1 0 32 30 40 1.5 1 0 40 31 44 1.5 1 0 44 32 29 1.5 1 0 29 33 25 1.5 1 0 25 34 36 1.5 1 0 36 35 36 1.5 1 0 36 36 40 1.5 1 0 40 37 24 1.5 1 0 24 38 28 1.5 1 0 28 39 31 1.5 1 1 30 40 46 1.5 1 0 46 41 32 1.5 1 0 32 42 41 1.5 1 0 41 43 43 1.5 1 0 43 44 24 1.5 1 0 24 45 32 1.5 1 0 32 46 28 1.5 1 0 28 47 34 1.5 1 0 34 48 40 1.5 1 0 40 49 39 1.5 1 0 39 50 33 1.5 1 0 33 51 30 1.5 1 0 30 52 38 1.5 1 0 38 53 30 1.5 1 0 30 54 30 1.5 1 1 29 55 21 1.5 1 0 21 56 33 1.5 1 0 33 57 28 1.5 1 0 28 58 26 1.5 1 0 26 59 26 1.5 1 0 26 60 27 1.5 1 0 27 61 26 1.5 1 0 26 62 30 1.5 1 0 30 63 13 1.5 1 0 13 64 29 1.5 1 0 29 65 16 1.5 1 0 16 66 16 1.5 1 0 16 67 21 1.5 1 0 21 68 13 1.5 1 0 13 69 31 1.5 1 0 31 70 21 1.5 1 0 21 71 18 1.5 1 0 18 72 21 1.5 1 0 21 73 26 1.5 1 0 26 74 27 1.5 1 0 27 75 27 1.5 1 0 27 76 21 1.5 1 0 21 77 25 1.5 1 0 25 78 19 1.5 1 0 19 79 23 1.5 1 0 23 80 17 1.5 1 0 17 81 22 1.5 1 0 22 82 24 1.5 1 0 24 83 13 1.5 1 0 13 84 20 1.5 1 0 20 85 19 1.5 1 0 19 86 28 1.5 1 0 28 87 26 1.5 1 0 26 88 17 1.5 1 0 17 89 15 1.5 1 0 15 90 12 1.5 1 0 12 91 17 1.5 1 0 17 92 21 1.5 1 0 21 93 11 1.5 1 0 11 94 17 1.5 1 0 17 95 17 1.5 1 0 17 96 10 1.5 1 0 10 97 11 1.5 1 0 11 98 14 1.5 1 0 14 99 7 1.5 1 0 7 100 3 1.5 1 0 3 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_4_s1_R1.fastq.gz ============================================= 24341968 sequences processed in total