SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_4_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_4_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 409.58 s (17 us/read; 3.57 M reads/minute). === Summary === Total reads processed: 24,341,968 Reads with adapters: 5,730,058 (23.5%) Reads written (passing filters): 24,341,968 (100.0%) Total basepairs processed: 2,138,379,836 bp Quality-trimmed: 7,229,586 bp (0.3%) Total written (filtered): 2,123,664,226 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5730058 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.1% C: 12.5% G: 34.6% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4437637 6085492.0 0 4437637 2 894680 1521373.0 0 894680 3 373576 380343.2 0 373576 4 11988 95085.8 0 11988 5 7986 23771.5 0 7986 6 2794 5942.9 0 2794 7 175 1485.7 0 175 8 175 371.4 0 175 9 222 92.9 0 33 189 10 243 23.2 1 4 239 11 65 5.8 1 1 64 12 8 1.5 1 0 8 13 5 1.5 1 0 5 14 3 1.5 1 0 3 15 2 1.5 1 0 2 16 6 1.5 1 0 6 17 8 1.5 1 0 8 18 8 1.5 1 0 8 19 13 1.5 1 0 13 20 8 1.5 1 0 8 21 3 1.5 1 0 3 22 2 1.5 1 0 2 23 9 1.5 1 0 9 24 6 1.5 1 0 6 25 7 1.5 1 0 7 26 12 1.5 1 0 12 27 23 1.5 1 1 22 28 11 1.5 1 0 11 29 11 1.5 1 0 11 30 2 1.5 1 0 2 31 2 1.5 1 0 2 32 11 1.5 1 0 11 33 2 1.5 1 0 2 34 7 1.5 1 0 7 35 7 1.5 1 0 7 36 4 1.5 1 0 4 37 4 1.5 1 0 4 38 4 1.5 1 0 4 39 5 1.5 1 0 5 40 4 1.5 1 0 4 41 3 1.5 1 0 3 42 5 1.5 1 0 5 43 3 1.5 1 0 3 44 6 1.5 1 0 6 45 10 1.5 1 0 10 46 13 1.5 1 0 13 47 18 1.5 1 0 18 48 4 1.5 1 0 4 49 6 1.5 1 0 6 50 13 1.5 1 0 13 51 12 1.5 1 0 12 52 9 1.5 1 0 9 53 14 1.5 1 0 14 54 1 1.5 1 0 1 55 11 1.5 1 0 11 56 4 1.5 1 0 4 57 6 1.5 1 0 6 58 2 1.5 1 0 2 59 5 1.5 1 0 5 60 2 1.5 1 0 2 61 4 1.5 1 0 4 62 4 1.5 1 0 4 63 6 1.5 1 0 6 64 4 1.5 1 0 4 65 4 1.5 1 0 4 66 2 1.5 1 0 2 67 7 1.5 1 1 6 68 1 1.5 1 0 1 69 7 1.5 1 0 7 70 4 1.5 1 0 4 71 6 1.5 1 0 6 72 2 1.5 1 0 2 73 12 1.5 1 0 12 74 2 1.5 1 0 2 75 6 1.5 1 0 6 76 11 1.5 1 0 11 77 2 1.5 1 0 2 78 6 1.5 1 0 6 79 3 1.5 1 0 3 80 7 1.5 1 0 7 81 6 1.5 1 0 6 82 7 1.5 1 0 7 83 6 1.5 1 0 6 84 5 1.5 1 0 5 85 5 1.5 1 0 5 86 6 1.5 1 0 6 87 4 1.5 1 0 4 88 5 1.5 1 0 5 89 4 1.5 1 0 4 90 7 1.5 1 0 7 91 1 1.5 1 0 1 92 2 1.5 1 0 2 93 1 1.5 1 0 1 94 3 1.5 1 0 3 95 3 1.5 1 0 3 96 3 1.5 1 0 3 97 3 1.5 1 0 3 98 2 1.5 1 0 2 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_4_s1_R2.fastq.gz ============================================= 24341968 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24341968 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 176698 (0.73%)