SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_6_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_6_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 407.37 s (17 us/read; 3.57 M reads/minute). === Summary === Total reads processed: 24,237,290 Reads with adapters: 5,603,158 (23.1%) Reads written (passing filters): 24,237,290 (100.0%) Total basepairs processed: 2,140,665,258 bp Quality-trimmed: 7,420,892 bp (0.3%) Total written (filtered): 2,125,867,555 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5603158 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.3% C: 13.4% G: 34.3% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4305035 6059322.5 0 4305035 2 895820 1514830.6 0 895820 3 376833 378707.7 0 376833 4 12244 94676.9 0 12244 5 8415 23669.2 0 8415 6 3206 5917.3 0 3206 7 186 1479.3 0 186 8 162 369.8 0 162 9 239 92.5 0 31 208 10 291 23.1 1 9 282 11 84 5.8 1 1 83 12 5 1.4 1 0 5 13 6 1.4 1 0 6 14 5 1.4 1 0 5 15 7 1.4 1 0 7 16 7 1.4 1 0 7 17 8 1.4 1 0 8 18 10 1.4 1 0 10 19 12 1.4 1 0 12 20 2 1.4 1 0 2 21 6 1.4 1 0 6 22 14 1.4 1 0 14 23 17 1.4 1 0 17 24 8 1.4 1 0 8 25 6 1.4 1 0 6 26 10 1.4 1 0 10 27 25 1.4 1 0 25 28 8 1.4 1 0 8 29 8 1.4 1 0 8 30 10 1.4 1 0 10 31 11 1.4 1 0 11 32 8 1.4 1 0 8 33 5 1.4 1 0 5 34 7 1.4 1 0 7 35 13 1.4 1 0 13 36 16 1.4 1 0 16 37 9 1.4 1 0 9 38 10 1.4 1 0 10 39 13 1.4 1 0 13 40 6 1.4 1 0 6 41 8 1.4 1 1 7 42 7 1.4 1 0 7 43 6 1.4 1 0 6 44 7 1.4 1 0 7 45 15 1.4 1 0 15 46 18 1.4 1 0 18 47 9 1.4 1 0 9 48 7 1.4 1 0 7 49 8 1.4 1 0 8 50 11 1.4 1 0 11 51 13 1.4 1 0 13 52 11 1.4 1 0 11 53 16 1.4 1 0 16 54 10 1.4 1 0 10 55 7 1.4 1 0 7 56 7 1.4 1 0 7 57 6 1.4 1 0 6 58 7 1.4 1 0 7 59 5 1.4 1 0 5 60 6 1.4 1 0 6 61 5 1.4 1 0 5 62 5 1.4 1 0 5 63 19 1.4 1 0 19 64 14 1.4 1 0 14 65 7 1.4 1 0 7 66 7 1.4 1 0 7 67 1 1.4 1 0 1 68 3 1.4 1 0 3 69 5 1.4 1 0 5 70 9 1.4 1 0 9 71 4 1.4 1 0 4 72 5 1.4 1 0 5 73 8 1.4 1 0 8 74 6 1.4 1 0 6 75 5 1.4 1 0 5 76 2 1.4 1 0 2 77 2 1.4 1 0 2 78 7 1.4 1 0 7 79 4 1.4 1 0 4 80 6 1.4 1 0 6 81 3 1.4 1 0 3 82 2 1.4 1 0 2 83 3 1.4 1 0 3 84 3 1.4 1 0 3 85 7 1.4 1 0 7 86 4 1.4 1 0 4 87 3 1.4 1 0 3 88 4 1.4 1 0 4 89 4 1.4 1 0 4 90 2 1.4 1 0 2 91 3 1.4 1 0 3 92 3 1.4 1 0 3 93 3 1.4 1 0 3 94 2 1.4 1 0 2 95 8 1.4 1 0 8 96 4 1.4 1 0 4 97 1 1.4 1 0 1 98 2 1.4 1 0 2 99 1 1.4 1 0 1 100 1 1.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_6_s1_R2.fastq.gz ============================================= 24237290 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24237290 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 157171 (0.65%)