SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_18_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_18_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1049.98 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 55,559,681 Reads with adapters: 22,333,371 (40.2%) Reads written (passing filters): 55,559,681 (100.0%) Total basepairs processed: 2,797,597,463 bp Quality-trimmed: 2,697,516 bp (0.1%) Total written (filtered): 2,771,263,695 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22333371 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.0% C: 10.9% G: 3.5% T: 38.0% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 21444400 13889920.2 0 21444400 2 578360 3472480.1 0 578360 3 244932 868120.0 0 244932 4 53822 217030.0 0 53822 5 6117 54257.5 0 6117 6 628 13564.4 0 628 7 1872 3391.1 0 1872 8 655 847.8 0 655 9 371 211.9 0 27 344 10 865 53.0 1 10 855 11 285 13.2 1 31 254 12 142 3.3 1 1 141 13 71 0.8 1 0 71 14 64 0.8 1 0 64 15 76 0.8 1 0 76 16 170 0.8 1 0 170 17 266 0.8 1 0 266 18 201 0.8 1 0 201 19 26 0.8 1 0 26 20 6 0.8 1 0 6 21 4 0.8 1 0 4 22 3 0.8 1 0 3 23 4 0.8 1 0 4 24 6 0.8 1 0 6 25 3 0.8 1 0 3 26 9 0.8 1 0 9 27 2 0.8 1 0 2 28 1 0.8 1 0 1 29 4 0.8 1 0 4 31 2 0.8 1 0 2 32 1 0.8 1 0 1 33 1 0.8 1 0 1 35 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_18_s456.fastq.gz ============================================= 55559681 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 511575 (0.9%)