SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_7_s456.fastq.gz Trimming mode: single-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: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16 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 AGATCGGAAGAGC zr1394_7_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 962.12 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 50,399,353 Reads with adapters: 20,325,988 (40.3%) Reads written (passing filters): 50,399,353 (100.0%) Total basepairs processed: 2,532,578,583 bp Quality-trimmed: 2,675,889 bp (0.1%) Total written (filtered): 2,508,324,225 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20325988 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.8% G: 3.8% T: 38.5% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 19528112 12599838.2 0 19528112 2 499729 3149959.6 0 499729 3 233073 787489.9 0 233073 4 47951 196872.5 0 47951 5 6971 49218.1 0 6971 6 678 12304.5 0 678 7 1959 3076.1 0 1959 8 1002 769.0 0 1002 9 471 192.3 0 58 413 10 855 48.1 1 19 836 11 465 12.0 1 57 408 12 302 3.0 1 4 298 13 133 0.8 1 0 133 14 127 0.8 1 0 127 15 216 0.8 1 0 216 16 561 0.8 1 0 561 17 1592 0.8 1 0 1592 18 1378 0.8 1 0 1378 19 143 0.8 1 0 143 20 22 0.8 1 0 22 21 16 0.8 1 0 16 22 6 0.8 1 0 6 23 12 0.8 1 0 12 24 16 0.8 1 0 16 25 15 0.8 1 0 15 26 33 0.8 1 0 33 27 32 0.8 1 0 32 28 21 0.8 1 0 21 29 5 0.8 1 0 5 30 10 0.8 1 0 10 31 18 0.8 1 0 18 32 23 0.8 1 0 23 33 15 0.8 1 0 15 34 15 0.8 1 0 15 35 7 0.8 1 0 7 36 2 0.8 1 0 2 37 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_7_s456.fastq.gz ============================================= 50399353 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 669240 (1.3%)