SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_2_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_2_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 881.68 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 46,666,438 Reads with adapters: 18,885,170 (40.5%) Reads written (passing filters): 46,666,438 (100.0%) Total basepairs processed: 2,346,424,714 bp Quality-trimmed: 2,397,497 bp (0.1%) Total written (filtered): 2,323,928,233 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18885170 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.3% C: 10.8% G: 3.9% T: 38.3% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 18095290 11666609.5 0 18095290 2 496013 2916652.4 0 496013 3 231867 729163.1 0 231867 4 47968 182290.8 0 47968 5 5845 45572.7 0 5845 6 652 11393.2 0 652 7 1874 2848.3 0 1874 8 729 712.1 0 729 9 427 178.0 0 33 394 10 865 44.5 1 9 856 11 376 11.1 1 57 319 12 209 2.8 1 0 209 13 100 0.7 1 0 100 14 99 0.7 1 0 99 15 182 0.7 1 0 182 16 439 0.7 1 0 439 17 1067 0.7 1 0 1067 18 932 0.7 1 0 932 19 83 0.7 1 0 83 20 22 0.7 1 0 22 21 7 0.7 1 0 7 22 14 0.7 1 0 14 23 6 0.7 1 0 6 24 6 0.7 1 0 6 25 13 0.7 1 0 13 26 16 0.7 1 0 16 27 8 0.7 1 0 8 28 8 0.7 1 0 8 29 13 0.7 1 0 13 30 3 0.7 1 0 3 31 8 0.7 1 0 8 32 12 0.7 1 0 12 33 7 0.7 1 0 7 34 6 0.7 1 0 6 35 1 0.7 1 0 1 36 1 0.7 1 0 1 37 1 0.7 1 0 1 39 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_2_s456.fastq.gz ============================================= 46666438 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 561298 (1.2%)