SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_5_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_5_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 563.29 s (18 us/read; 3.38 M reads/minute). === Summary === Total reads processed: 31,778,715 Reads with adapters: 6,846,951 (21.5%) Reads written (passing filters): 31,778,715 (100.0%) Total basepairs processed: 2,877,311,782 bp Quality-trimmed: 9,863,732 bp (0.3%) Total written (filtered): 2,858,374,133 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6846951 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.3% C: 13.4% G: 33.2% T: 31.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5229812 7944678.8 0 5229812 2 1095891 1986169.7 0 1095891 3 489213 496542.4 0 489213 4 15569 124135.6 0 15569 5 10559 31033.9 0 10559 6 4110 7758.5 0 4110 7 221 1939.6 0 221 8 231 484.9 0 231 9 248 121.2 0 46 202 10 275 30.3 1 1 274 11 71 7.6 1 0 71 12 10 1.9 1 0 10 13 11 1.9 1 0 11 14 15 1.9 1 0 15 15 10 1.9 1 0 10 16 13 1.9 1 0 13 17 7 1.9 1 0 7 18 10 1.9 1 0 10 19 9 1.9 1 0 9 20 10 1.9 1 0 10 21 11 1.9 1 0 11 22 12 1.9 1 0 12 23 18 1.9 1 0 18 24 11 1.9 1 0 11 25 7 1.9 1 0 7 26 13 1.9 1 0 13 27 32 1.9 1 0 32 28 18 1.9 1 0 18 29 7 1.9 1 0 7 30 9 1.9 1 0 9 31 10 1.9 1 0 10 32 11 1.9 1 0 11 33 5 1.9 1 0 5 34 15 1.9 1 0 15 35 10 1.9 1 0 10 36 6 1.9 1 0 6 37 4 1.9 1 0 4 38 10 1.9 1 0 10 39 9 1.9 1 0 9 40 11 1.9 1 0 11 41 12 1.9 1 0 12 42 11 1.9 1 0 11 43 6 1.9 1 0 6 44 10 1.9 1 0 10 45 15 1.9 1 0 15 46 10 1.9 1 0 10 47 14 1.9 1 0 14 48 6 1.9 1 0 6 49 7 1.9 1 0 7 50 8 1.9 1 0 8 51 14 1.9 1 0 14 52 16 1.9 1 1 15 53 15 1.9 1 0 15 54 12 1.9 1 0 12 55 10 1.9 1 0 10 56 6 1.9 1 0 6 57 8 1.9 1 0 8 58 9 1.9 1 0 9 59 3 1.9 1 0 3 60 4 1.9 1 0 4 61 10 1.9 1 0 10 62 5 1.9 1 0 5 63 10 1.9 1 0 10 64 6 1.9 1 1 5 65 11 1.9 1 0 11 66 7 1.9 1 0 7 67 1 1.9 1 0 1 68 8 1.9 1 0 8 69 6 1.9 1 0 6 70 12 1.9 1 0 12 71 5 1.9 1 0 5 72 6 1.9 1 0 6 73 4 1.9 1 0 4 74 8 1.9 1 0 8 75 9 1.9 1 0 9 76 8 1.9 1 0 8 77 10 1.9 1 0 10 78 5 1.9 1 0 5 79 3 1.9 1 0 3 80 4 1.9 1 0 4 81 7 1.9 1 0 7 82 7 1.9 1 0 7 83 14 1.9 1 0 14 84 10 1.9 1 0 10 85 6 1.9 1 0 6 86 3 1.9 1 0 3 87 3 1.9 1 0 3 88 4 1.9 1 0 4 89 5 1.9 1 0 5 90 5 1.9 1 0 5 91 5 1.9 1 0 5 92 3 1.9 1 0 3 93 2 1.9 1 0 2 94 4 1.9 1 0 4 95 6 1.9 1 0 6 96 4 1.9 1 0 4 97 4 1.9 1 0 4 98 1 1.9 1 0 1 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_5_s1_R2.fastq.gz ============================================= 31778715 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 31778715 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 148997 (0.47%)