SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_3_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_3_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 542.22 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 29,892,002 Reads with adapters: 13,088,943 (43.8%) Reads written (passing filters): 29,892,002 (100.0%) Total basepairs processed: 2,698,353,334 bp Quality-trimmed: 8,120,692 bp (0.3%) Total written (filtered): 2,674,123,947 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13088943 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.1% C: 6.8% G: 22.4% T: 43.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11066739 7473000.5 0 11066739 2 1369931 1868250.1 0 1369931 3 522764 467062.5 0 522764 4 82767 116765.6 0 82767 5 30112 29191.4 0 30112 6 8805 7297.9 0 8805 7 3969 1824.5 0 3969 8 96 456.1 0 96 9 69 114.0 0 12 57 10 158 28.5 1 1 157 11 106 7.1 1 0 106 12 56 1.8 1 0 56 13 57 1.8 1 0 57 14 100 1.8 1 0 100 15 40 1.8 1 0 40 16 41 1.8 1 0 41 17 37 1.8 1 0 37 18 60 1.8 1 0 60 19 44 1.8 1 0 44 20 47 1.8 1 0 47 21 45 1.8 1 1 44 22 45 1.8 1 0 45 23 64 1.8 1 2 62 24 38 1.8 1 0 38 25 53 1.8 1 0 53 26 68 1.8 1 0 68 27 45 1.8 1 0 45 28 60 1.8 1 0 60 29 46 1.8 1 0 46 30 71 1.8 1 0 71 31 41 1.8 1 0 41 32 47 1.8 1 0 47 33 50 1.8 1 0 50 34 40 1.8 1 0 40 35 49 1.8 1 0 49 36 37 1.8 1 0 37 37 35 1.8 1 0 35 38 43 1.8 1 0 43 39 52 1.8 1 0 52 40 43 1.8 1 0 43 41 58 1.8 1 0 58 42 55 1.8 1 0 55 43 40 1.8 1 0 40 44 36 1.8 1 0 36 45 33 1.8 1 0 33 46 48 1.8 1 0 48 47 37 1.8 1 0 37 48 42 1.8 1 0 42 49 42 1.8 1 0 42 50 40 1.8 1 0 40 51 37 1.8 1 1 36 52 46 1.8 1 0 46 53 37 1.8 1 0 37 54 45 1.8 1 0 45 55 43 1.8 1 1 42 56 38 1.8 1 0 38 57 38 1.8 1 0 38 58 41 1.8 1 0 41 59 36 1.8 1 0 36 60 44 1.8 1 1 43 61 32 1.8 1 0 32 62 33 1.8 1 0 33 63 31 1.8 1 0 31 64 52 1.8 1 0 52 65 27 1.8 1 0 27 66 37 1.8 1 0 37 67 31 1.8 1 0 31 68 24 1.8 1 0 24 69 45 1.8 1 0 45 70 33 1.8 1 0 33 71 36 1.8 1 0 36 72 34 1.8 1 0 34 73 32 1.8 1 0 32 74 39 1.8 1 0 39 75 32 1.8 1 0 32 76 20 1.8 1 0 20 77 34 1.8 1 0 34 78 34 1.8 1 0 34 79 31 1.8 1 0 31 80 27 1.8 1 0 27 81 22 1.8 1 0 22 82 25 1.8 1 0 25 83 42 1.8 1 0 42 84 32 1.8 1 0 32 85 24 1.8 1 0 24 86 32 1.8 1 1 31 87 44 1.8 1 0 44 88 32 1.8 1 0 32 89 16 1.8 1 0 16 90 25 1.8 1 0 25 91 32 1.8 1 0 32 92 22 1.8 1 0 22 93 28 1.8 1 0 28 94 22 1.8 1 0 22 95 7 1.8 1 0 7 96 24 1.8 1 0 24 97 16 1.8 1 0 16 98 20 1.8 1 1 19 99 7 1.8 1 0 7 100 1 1.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_3_s1_R1.fastq.gz ============================================= 29892002 sequences processed in total