SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_17_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_17_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 798.85 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 42,730,485 Reads with adapters: 16,838,546 (39.4%) Reads written (passing filters): 42,730,485 (100.0%) Total basepairs processed: 2,143,526,203 bp Quality-trimmed: 2,502,691 bp (0.1%) Total written (filtered): 2,123,026,980 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16838546 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 11.5% G: 4.6% T: 37.8% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 16087858 10682621.2 0 16087858 2 461836 2670655.3 0 461836 3 232097 667663.8 0 232097 4 41330 166916.0 0 41330 5 7514 41729.0 0 7514 6 690 10432.2 0 690 7 1822 2608.1 0 1822 8 1037 652.0 0 1037 9 422 163.0 0 61 361 10 920 40.8 1 8 912 11 430 10.2 1 86 344 12 213 2.5 1 0 213 13 151 0.6 1 0 151 14 137 0.6 1 0 137 15 184 0.6 1 0 184 16 404 0.6 1 0 404 17 816 0.6 1 0 816 18 502 0.6 1 0 502 19 62 0.6 1 0 62 20 18 0.6 1 0 18 21 3 0.6 1 0 3 22 13 0.6 1 0 13 23 11 0.6 1 0 11 24 6 0.6 1 0 6 25 7 0.6 1 0 7 26 12 0.6 1 0 12 27 15 0.6 1 0 15 28 4 0.6 1 0 4 29 4 0.6 1 0 4 30 4 0.6 1 0 4 31 3 0.6 1 0 3 32 3 0.6 1 0 3 33 4 0.6 1 0 4 34 6 0.6 1 0 6 35 5 0.6 1 0 5 36 1 0.6 1 0 1 37 2 0.6 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_17_s456.fastq.gz ============================================= 42730485 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 659939 (1.5%)