SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_7_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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_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_7_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 557.90 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 29,534,746 Reads with adapters: 13,300,837 (45.0%) Reads written (passing filters): 29,534,746 (100.0%) Total basepairs processed: 2,711,811,528 bp Quality-trimmed: 8,678,708 bp (0.3%) Total written (filtered): 2,686,940,853 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13300837 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 28.0% C: 6.4% G: 21.3% T: 44.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11345362 7383686.5 0 11345362 2 1348726 1845921.6 0 1348726 3 476512 461480.4 0 476512 4 81590 115370.1 0 81590 5 31877 28842.5 0 31877 6 9281 7210.6 0 9281 7 4185 1802.7 0 4185 8 72 450.7 0 72 9 56 112.7 0 10 46 10 135 28.2 1 1 134 11 78 7.0 1 0 78 12 49 1.8 1 0 49 13 55 1.8 1 0 55 14 81 1.8 1 0 81 15 34 1.8 1 0 34 16 33 1.8 1 0 33 17 47 1.8 1 0 47 18 48 1.8 1 0 48 19 37 1.8 1 0 37 20 31 1.8 1 0 31 21 35 1.8 1 0 35 22 41 1.8 1 0 41 23 59 1.8 1 1 58 24 34 1.8 1 0 34 25 30 1.8 1 1 29 26 57 1.8 1 0 57 27 46 1.8 1 0 46 28 47 1.8 1 1 46 29 37 1.8 1 0 37 30 53 1.8 1 0 53 31 39 1.8 1 0 39 32 46 1.8 1 0 46 33 43 1.8 1 0 43 34 45 1.8 1 0 45 35 35 1.8 1 0 35 36 33 1.8 1 0 33 37 27 1.8 1 0 27 38 31 1.8 1 0 31 39 34 1.8 1 0 34 40 38 1.8 1 0 38 41 32 1.8 1 0 32 42 60 1.8 1 0 60 43 35 1.8 1 0 35 44 29 1.8 1 0 29 45 34 1.8 1 0 34 46 21 1.8 1 0 21 47 32 1.8 1 0 32 48 43 1.8 1 0 43 49 46 1.8 1 0 46 50 48 1.8 1 0 48 51 33 1.8 1 0 33 52 32 1.8 1 0 32 53 33 1.8 1 0 33 54 45 1.8 1 0 45 55 51 1.8 1 0 51 56 32 1.8 1 0 32 57 39 1.8 1 0 39 58 38 1.8 1 0 38 59 32 1.8 1 0 32 60 37 1.8 1 0 37 61 22 1.8 1 0 22 62 36 1.8 1 0 36 63 33 1.8 1 0 33 64 34 1.8 1 0 34 65 41 1.8 1 0 41 66 36 1.8 1 0 36 67 33 1.8 1 1 32 68 28 1.8 1 0 28 69 25 1.8 1 0 25 70 19 1.8 1 0 19 71 33 1.8 1 0 33 72 21 1.8 1 0 21 73 20 1.8 1 0 20 74 28 1.8 1 1 27 75 25 1.8 1 0 25 76 30 1.8 1 0 30 77 25 1.8 1 0 25 78 35 1.8 1 0 35 79 31 1.8 1 0 31 80 34 1.8 1 0 34 81 22 1.8 1 0 22 82 22 1.8 1 0 22 83 29 1.8 1 0 29 84 27 1.8 1 0 27 85 21 1.8 1 0 21 86 27 1.8 1 0 27 87 29 1.8 1 0 29 88 18 1.8 1 0 18 89 17 1.8 1 0 17 90 25 1.8 1 0 25 91 21 1.8 1 0 21 92 19 1.8 1 0 19 93 18 1.8 1 0 18 94 16 1.8 1 0 16 95 15 1.8 1 0 15 96 19 1.8 1 0 19 97 19 1.8 1 0 19 98 19 1.8 1 0 19 99 11 1.8 1 0 11 100 3 1.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_7_s1_R1.fastq.gz ============================================= 29534746 sequences processed in total